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PeptGen: Designing Peptides for Immunological Studies
and Application to HIV Consensus Sequences

Charles Calef(1), Rama Thakallapally(1), Dorothy Lang(1), Christian Brander(2), Philip Goulder(3), Otto Yang(4), Bette Korber(1)

  1. Theoretical Biology and Biophysics (T10), Los Alamos National Laboratory, Los Alamos, NM 87545
  2. Partners AIDS Research Center, Massachusetts General Hospital, Boston, MA
  3. John Radcliffe Hospital, Oxford OX3 9DS, U.K.
  4. AIDS Institute, UCLA Medical Center, Los Angeles, CA 90095

Abstract

PeptGen is a Web-based tool that enables users to subdivide protein sequences into shorter overlapping peptides according to user-specified criteria. Immunologists can use it to generate peptide sequences for immunological analysis according to a consistent set of rules. As an example, this tool was applied to the HIV-1 B subtype consensus sequences of Pol, Gag, Env, and the HIV regulatory proteins. A stringent set of rules was followed that prohibited certain amino acids from occurring at the N- and C-terminal positions. These ``forbidden'' amino acids were problematic either in terms of peptide chemistry or in terms of being unlikely to serve as anchor residues for binding to class I MHC proteins. This peptide set is meant to serve as an example and users can select their own parameters and protein sequences (HIV or other proteins) as input for the interactive Web version of the program. The use of consensus sequences for generation of testing reagents, versus laboratory strains, is discussed. The consensus sequence more closely resembles currently circulating forms than any one isolate resembles other circulating forms, so would be more likely to elicit a cross-reactive CTL response. An alignment for comparison of all major subtype consensus sequences, the global consensus, and two B subtype isolates is provided. Consensus sequences for all HIV-1 subtypes and for all HIV-1 proteins are available at the PeptGen Web site:

http://hiv.lanl.gov/content/sequence/PEPTGEN/peptgen.html

Immunologists frequently need to generate overlapping peptides to determine immunogenic regions and define T cell and contiguous antibody epitopes within a protein. We have designed a simple tool with a web interface to facilitate this process. The user inputs a protein sequence, and specifies the length of peptide and the extent of the overlap. In the past a typical HIV study might involve a single protein serially broken down into peptides 20 amino acids in length with an overlap of 10 amino acids. The initial determination of reactive peptides would be followed by subsequent fine mapping within the reactive peptides to more precisely define the optimal epitope. Because of recent experimental advances [Kaul & Rowland-Jones(1999)] it has become possible to use smaller peptides that more closely identify the reactive epitope in the first screening, as well as to perform a more comprehensive examination of many HIV proteins in the context of a single study.

It occurred to us that it would be helpful to provide a Web-based tool that could neatly map out overlapping peptides that follow a set of pre-specified rules. In particular, for CTL studies, it may be advantageous to modify peptides lengths when amino acids that are unlikely to serve as C-terminal anchor residues fall in the C terminal position in a peptide. Additionally, certain amino acids could be forbidden based on the pragmatic difficulties related to peptide synthesis. The variables that the user may specify are


1.
peptide length
2.
peptide overlap
3.
forbidden amino acids at the C- and N-terminal ends of a peptide
4.
how much to shorten or lengthen the peptide in search of allowed terminal amino acids.


The output yields a list of peptides generated according to the users intentions. The Kyte-Doolittle hydropathy score for the peptide may be provided (Chuck add ref), and the amino acids in the peptides can be colored according to a hydrophobicity scale or according to amino acid side-chain chemistry if desired.

Given an amino acid sequence, PeptGen splits the sequence into shorter overlapping peptide fragments and displays them. Figure 1 shows what part of the output might look like. The first line is the submitted amino acid sequence, while the peptides generated by the program form the stair-step pattern below. The submitted protein sequence may have spaces and newline characters within


Word length:

18

Represent all n-mers of length:

11

Forbidden C-term characters:

GPEDQNTSC

Forbidden N-term characters:

Q

Shorten by:

3

Lengthen by:

2







MGARASvLSggeLDrWEkiRLRPgGkKkYkLKHivWASRELERFavnpgLLEtseGCrQIlgQLqpsLqTGSEelrSlyNtvAtLYCvHqrievkDTKeAl

MGARASvLSggeLDrWEk (18) [-0.54]

        SggeLDrWEkiRLRPgGk (18) [-1.37]

                EkiRLRPgGkKkYkLKHi (18) [-1.46]

                        GkKkYkLKHivWASREL (17) [-0.94]

                               KHivWASRELERFav (15) [-0.11]

                                    ASRELERFavnpgLL (15) [-0.02]

                                         ERFavnpgLLEtseGCr(17) [-0.47]

                                                gLLEtseGCrQIlgQL(16) [0.06]

                                                      eGCrQIlgQLqpsLqTGS (18) [-0.48] All C-term amino acids forbidden

                                                             gQLqpsLqTGSEelrSly (18) [-0.76]

                                                                     TGSEelrSlyNtvAtLY (17) [-0.25]

                                                                            SlyNtvAtLYCvHqriev (18) [0.33]

                                                                                    LYCvHqrievkDTKeAl (17) [-0.39]









Figure 1. Sample PeptGen output for part of the HIV-1 Gag Consensus B protein.

it, but these (and a few other ``funny characters'') will be removed. The number in parentheses following each peptide records the length of the peptide. In this particular example, the user had specified that the program first attempt pto construct peptides of 18 amino acids, which we will refer to as the ``ideal'' length.

Why then are some of the peptides shorter than 18 amino acids? Because the user also specified a list of amino acids that are ``forbidden" to occur at the C-terminus because of their inimical effect on binding to class I molecules. Forbidden amino acids are underlined and printed in bold. In this run the forbidden amino acids were declared to be ``GPEDQNTSC". Note, forbidden amino acids can be entered as either capital letters or lowercase letters so GpeDqnTSc would give you the same results.

As you can see the fourth peptide in Figure 1 is only 17 AAs-long because the 18th amino acid is a ``E", a member of the forbidden set. The fifth peptide is only 15 amino acids long because amino acids 16, 17, and 18 are N, P, and G, all forbidden. The first position at which non-forbidden amino acid is found determines the length of the peptide. How much the program will shorten the peptide in its search for an allowed amino acid is specified by the user. In this example the ``shorten by" parameter was set to 3. If all the amino acids from 18 down to 15 are forbidden, then the program begins to lengthen the peptide beyond the ideal of 18, one amino acid at a time until it finds an allowed amino acid. It will add amino acids to the peptide up to the limit set by the ``lengthen by" parameter (2 in this case). If all amino acids between between 15 and 20 are forbidden, then the 18-mer is used even though it ends in a forbidden amino acid. Such peptides-one of which is shown in Figure 1-are marked with the words ``All C-term amino acids forbidden". The number of times such ``forbidden" peptides are generated is reported at the end of your output. In the peptides only the forbidden amino acids near the C-terminus are printed in bold and underlined in the peptide, but all forbidden amino acids are underlined in the reference strain.

The rarely-invoked "Proline rule'' says that a peptide may never end in a proline residue. In this sense proline may be thought of as ultra-forbidden. If all the AAs near the C-terminus are forbidden, the program selects the peptide of ïdeal length" (18-mer in the examples above) even though it ends with a forbidden AA. But if the proline rule is being observed and the eighteenth AA is proline then the 17-mer will be chosen as the peptide. Under the proline rule the algorithm will shorten the ideal peptide and then lengthen it searching for non-proline AAs. If all AAs at the C-term are prolines this is reported and the 18-mer would be used.

The user may also specify a forbidden character(s) at the N terminus. Because of difficulties of synthesizing peptides that initiate with an N-terminal Glutamine (Q), that is the default forbidden character. If after shifting right the proper amount to begin the next peptide the program detects an N-terminal Q it will back up one position and try to generate a peptide from that starting position, and so on until it finds a non-Q start. It is possible that given severe constraints on the N- and C-terminal amino acids that a peptide cannot be generated. In this case the program terminates and suggests you adjust your constraints.

The overlap determines how many amino acids are shared between adjacent peptides. In the example, the word length was set to 18, the overlap was set to 10. With an overlap of 10, every 11-mer will be represented exactly once as illustrated in Figure 2. The reason for implementing this parameter is that in immunological studies it is usually the shorter peptides (9 to 11-mers) that are of most interest, but the cost and labor of generating every single one of these is prohibitive. As a compromise, longer peptides are synthesized in such a way to insure that shorter peptides of a given length (e.g. 11-mers) will be represented at least once in the longer peptides. The algorithm this program uses insures that this will be the case.

 


MGARASVLSGGELDRWEK (18)  first peptide



MGARASVLSGG

 GARASVLSGGE

  ARASVLSGGEL      -11-mers within 1st peptide

   RASVLSGGELD

    ASVLSGGELDR

     SVLSGGELDRW

      VLSGGELDRWE

       LSGGELDRWEK



        SGGELDRWEKIRLRPGGK (18)  second peptide



        SGGELDRWEKI

         GGELDRWEKIR

           GELDRWEKIRL

           ELDRWEKIRLR     -11-mers within 2nd peptide

            LDRWEKIRLRP

             DRWEKIRLRPG

              RWEKIRLRPGG

               WEKIRLRPGGK



                EKIRLRPGGKKKYKLKHI (18) third peptide


The user may exercise options to color the amino acids of the peptides according to Kyte-Doolittle hydropathy classes and to compute the average hydropathy score for each peptide. If these options are selected, the most hydrophobic will be colored red and the most hydrophilic blue, moving through the spectrum accordingly. The hydropathy score is printed in square brackets after each peptide.

Figure 3 shows the submission form for the PeptGen Web site. To use, paste your raw amino acid acid sequence into the large text box beneath the ``Sample Input" button. Below that box is a table with five rows which contain the default values of the adjustable parameters described above in this article. Change any of these parameters to your specifications and click on the "FIRE" button to submit your PeptGen request.

Epitopes can be missed due to differences between an infecting strain and the strain used to probe the immune response (Jin). In circumstances where it is not possible to use autologous strains to explore individual immune responses, there may be advantages in using HIV consensus sequences or modeled ancestral sequences as a basis for scanning for immunologically reactive peptides. In phylogenetic analysis, sequences from the same subtype tend to be approximately equidistant, with a tendency to have longer branch lengths relative to the ancestral node of the subtype as time goes on. There is a star-like pattern to these subtype groupings, such that there is often little clear phylogenetic structure within a subtype. Under these circumstances, a consensus sequence, comprising the most common amino acid found in a particular position, closely resembles the most recent common ancestor of the subtype. Because the consensus is ``central'', there are on average approximately half the number of amino acid differences between the consensus and a contemporary strains as there are between two contemporary strains (Figure 2). For example, there are 220 substitutions between B subtype sequences HXB2 and DH123 in the 856 amino acids of Envelope. But there are only 98 or 128 changes between HXB2 or DH123 and the B subtype consensus, respectively. A subtype consensus is also more similar to other subtypes than contemporary strain inter-subtype sequence relationships, which may be a consideration for vaccine design (i.e., a B subtype consensus would be more similar than would a contemporary B strain to a contemporary C strain.

The consensus of the subtype consensus sequences is not weighted for any one subtype, and through maximum likelihood phylogenetic analysis essentially mimics the M group ancestral sequence (Korber). This sequence is most central in the tree, and may be most appropriate for consideration of a single sequence with the greatest potential for global breadth of cross-reactivity to M group strains. The consensus sequence from all major HIV subtypes, and HIV-1 M group "consensus of the consensus" is be provided at the web site for user input.

For the sake of comparison, an alignment of all HIV proteins, including two subtype B reference strains, a consensus for each subtype, and the consensus of the consensus is provided. The B consensus is used as the input to PeptGen, with the peptide length of 18, and an overlap of 10, with the settings as in Figure 1.

[Kaul & Rowland-Jones(1999)] Rupert Kaul and Sarah L. Rowland-Jones, Methods of Detection of HIV-specific CTL and Their Role in Protection Against HIV Infection. In: Human Retroviruses and AIDS 1999: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Kuiken CL, Foley B, Hahn B, Korber B, McCutchan F, Marx PA, Mellors JW, Mullins JI, Sodroski J, and Wolinsky S, Eds. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM.


[Kyte & Doolittle(1982)] Jack Kyte and Russell F. Doolittle, A Simple Method for Displaying the Hydropathic Character of a Protein, J. Mol. Biol. 157:105-132.

[Jin(2000)] Jin X, Roberts CG, Nixon DF, Safrit JT, Zhang LQ, Huang YX, Bhardwaj N, Jesdale B, DeGroot AS, Koup RA Identification of subdominant cytotoxic T lymphocyte epitopes encoded by autologous HIV type 1 sequences, using dendritic cell stimulation and computer-driven algorithm, AIDS Res Hum Retroviruses 16(1):67-76.

[Korber(2000)] Korber, B, M Muldoon, J Theiler, F Gao, R Gupta, A Lapedes, B Hahn, S Wolinsky, T Bhattacharya, Timing the Ancestor of the HIV-1 Pandemic Strains, Science 288:1789-96.


Word length:

18

Overlap peptide by

10

Forbidden C-term characters:

GPEDQNTSC

Forbidden N-term characters:

Q

Shorten by:

3

Lengthen by:

2




Gag[Number of peptides generated: 67]

MGARASvLSggeLDrWEkiRLRPgGkKkYkLKHivWASRELERFavnpgLLEtseGCrQIlgQLqpsLqTGSEelrSlyNtvAtLYCvHqrievkDTKeAl  Gag Con-B

---------------------------------------------------------------------------------------------I-------  Gag HXB2

-----------K--S--------------------------------------------------------------------------E-----------  Gag DH123

-----------k--a--------------r---l-----------L--s----t---Q--me----A-k--T--------------------d--------  Gag Con-A

------I-R--K--k------------h-m---l-----------l-----------k--mk----A----T-----------------ag---r------  Gag Con-C

-----------K--a--------------r---l-----------L-----------k--i-----ai---------------------e-----------  Gag Con-D

-----------K--a--------------rm--L-----------lD----------qk-Ir-------------------i-V--y---k----------  Gag Con-F1

-----------K--A------------r-R-----------k---L--s----T---KK-I--------------K----aiVV--Y-----d-R------  Gag Con-F2

-----------K--a----------r---r---l-----------L--d----A---q--Ma----a----T--ik--f-----------k----------  Gag Con-G

-----------k--a--------------R---l-----------L-------a---l--ie----aiK--T---x--f----v--------d--------  Gag Con-H

------I----K--D------------q-RI--L-------D---L------SAK--Q---V----A----Tq-IK-----------------I-------  Gag Con-J

-----------K--a--------------r---L-----------l-------t------ir------------------------------qir------  Gag Con-K

-----------k--a--------------r---l-----------l-------a---q--me----a-k------k--f----------------------  Gag Con-O

-----------k--a--------------r---l-----------l-----------q--i-----a----------------------------------  Gag Con-Con

MGARASvLSggeLDrWEk (18) [-0.54] 

        SggeLDrWEkiRLRPgGk (18) [-1.37] 

                EkiRLRPgGkKkYkLKHi (18) [-1.46] 

                        GkKkYkLKHivWASREL (17) [-0.94] 

                               KHivWASRELERFav (15) [-0.11] 

                                    ASRELERFavnpgLL (15) [-0.02] 

                                         ERFavnpgLLEtseGCr (17) [-0.47] 

                                                gLLEtseGCrQIlgQL (16) [0.06] 

                                                      eGCrQIlgQLqpsLqTGS (18) [-0.48] All C-term AAs forbidden

                                                             gQLqpsLqTGSEelrSly (18) [-0.76] 

                                                                     TGSEelrSlyNtvAtLY (17) [-0.25] 

                                                                            SlyNtvAtLYCvHqriev (18) [0.33] 

                                                                                    LYCvHqrievkDTKeAl (17) [-0.39] 

ievkDTKeAlekiEEEQnkskkkaqqaaadtgnssqvSqNYPIVQNlqGQMVHQaiSpRTLnAWVKVvEEKAFSPEVIPMFsALsEGAtPQDLnTMLNTVGGHQAAMqMLK  Gag Con-B

--I-------D---------------------H-N-----------I----------------------------------------------------------------  Gag HXB2

----------D-V---------------------------------I--------L-------------------------------------------------------  Gag DH123

-d--------d----i-----Q-t-----------k----------A-------sl-----------i--------------------------m---i------------  Gag Con-A

---r------D---------qq-t------...kgk-------------------------------i-------------T-----------------------------  Gag Con-C

------------m------------------------------------------------------I-------------------------------------------  Gag Con-D

----------d-L-------qQ-T------....KG------------------s------------I-------------------------------------------  Gag Con-F1

-d-R------D-LQ---D-hQQ-t--.---..K-ke-------l--i--------L-----------I-------------------------------------------  Gag Con-F2

-----------EV-KI-K--Qq-i----.-e---n-----------A----------------------------------------------------------------  Gag Con-G

-d--------g----I---rqQ-T------KEkDnK----------A-----------------------------------------------A----------------  Gag Con-H

--I-------d----I---N-QQ--K-E.-KKDN----------------P----L-----------I-------------------------------I-----------  Gag Con-J

-qir------D-l-------qq-t------....kg------------------pL-----------I-------------------------------------------  Gag Con-K

----------d----i-----q-t-----.-----k----------a--------------------i--------------------------m---i------------  Gag Con-O

----------d---------qq-t-------------------------------------------i-------------------------------------------  Gag Con-Con

ievkDTKeAlekiEEEQnk (19) [-1.53] 

         lekiEEEQnkskkkaqqa (18) [-2.02] 

                 nkskkkaqqaaadtgnssqv (20) [-1.43] 

                           aadtgnssqvSqNYPIV (17) [-0.44] 

                                  sqvSqNYPIVQNlqGQMV (18) [-0.37] 

                                          IVQNlqGQMVHQaiSpR (17) [-0.18] 

                                                GQMVHQaiSpRTLnAWVK (18) [-0.24] 

                                                        SpRTLnAWVKVvEEKAF (17) [-0.24] 

                                                               WVKVvEEKAFSPEVIPMF (18) [0.41] 

                                                                       AFSPEVIPMFsALsEGA (17) [0.73] 

                                                                              PMFsALsEGAtPQDLnTM (18) [-0.16] 

                                                                                      GAtPQDLnTMLNTVGGH (17) [-0.39] 

                                                                                             nTMLNTVGGHQAAMqMLK (18) [-0.12] 

GHQAAMqMLKETINeEAaEWDRlHPvhAGpiaPGQMrePRGSDIAGtTSTLqeqIgWMTnnPpiPVGeIYKRWIIlGLNkIVRMYSPtsILDIrQGPKEpFRDYVDRFYKTLR  Gag Con-B

----------------------V------------------------------------------------------------------------------------------  Gag HXB2

---------------------------------------------------------------------------M-------------------------------------  Gag DH123

----------D--------------------p------------------p--------g-------D-------------------V-----k--------------F----  Gag Con-A

----------D--------------------------------------------a---s---v---d-------------------V-----k--------------F----  Gag Con-C

------------------------------v------------------------a---S---------------------------V-------------------------  Gag Con-D

----------D--------------------p-----------------------Q---s---V---d-------------------V--------------------F----  Gag Con-F1

----------D--------------------P-----------------------a---s---V-----------------------V-----K--------------F----  Gag Con-F2

----------d---d-------m--qQ----p---I-------------------r---s---------------------------V--------------------F----  Gag Con-G

----------D--------------------P-----------------------A---G-------D-------------------V-----K--------------F----  Gag Con-H

----------D-----------V------------V-----------------------G---------------------------V--------------------F-A--  Gag Con-J

----------d--------------------P-----------------------a---s---v-----------------------V--------------------f----  Gag Con-K

----------d-----------v--------p---------------------------s---------------------------v--------------------f----  Gag Con-O

----------d--------------------p-----------------------a---s---------------------------v--------------------f----  Gag Con-Con

GHQAAMqMLKETINeEAa (18) [-0.55] 

        LKETINeEAaEWDRlHPv (18) [-0.88] 

                AaEWDRlHPvhAGpia (16) [-0.17] 

                      lHPvhAGpiaPGQMrePR (18) [-0.64] 

                              iaPGQMrePRGSDIA (15) [-0.65] 

                                   MrePRGSDIAGtTSTL (16) [-0.63] 

                                         SDIAGtTSTLqeqIgWM (17) [-0.17] 

                                                STLqeqIgWMTnnPpiPV (18) [-0.38] 

                                                        WMTnnPpiPVGeIYKRWI (18) [-0.46] 

                                                                PVGeIYKRWIIlGLNkIV (18) [0.56] 

                                                                        WIIlGLNkIVRMYSPtsI (18) [0.74] 

                                                                                IVRMYSPtsILDIrQGPK (18) [-0.21] 

                                                                                        sILDIrQGPKEpFRDYV (17) [-0.75] 

                                                                                               GPKEpFRDYVDRFYKTLR (18) [-1.39] 

YVDRFYKTLRaEQAsQeVKNwmTETlLVQNaNPDCkTILKALGPaATLeeMMTACQGVGGPgHKARvlAEAMSqvtnsatiMmQrgNfrnqrktvKCfnCGKeGHiaknCrAPR  Gag Con-B

---------------------------------------------------------------------------------------------I-----------T-R------  Gag HXB2

------------------------------S-------------G-----------------------------I---------G--------I.-----------S-------  Gag DH123

-----F--------t----g----------------s--r---aG--------------------------------...---------G-.-rI----------L-r------  Gag Con-A

-----F--------t-d------d---------------r----g-s--------------s------------..---.-----s--Kgpkri-------------r------  Gag Con-C

----------------d---------------------------q----------------s------------.-------------KGp--ii-------------------  Gag Con-D

-----F-------------g---d--------------------G----------------s------------.--.-.----KS--kG--Ri-------------r------  Gag Con-F1

-----F--------T-----------------------------G----------------s----I------K.-s.-.----KS--KG--RI-------------R------  Gag Con-F2

-----F--------t----g---D---------------r----G----------------s------------.sGA-A----kS--KGP-R-I----------L-R------  Gag Con-G

-----F--------T-d------d---------------r---qG-SI-------------S---------------ana----K---KGp--i-------------R------  Gag Con-H

-----F-A------T-D------D-------------------SG--------------------------------TN.---------DHKRI--------Q-----------  Gag Con-J

-----f--------T--------d--------------------G-s-------------------i----------a..v-------KG---ii------------r------  Gag Con-K

-----f--------t-----------------------------g----------------s------------.q-an.--------kg-.-ri----------l-r------  Gag Con-O

-----f--------t--------d--------------------g----------------s---------------a-.--------kg---i-------------r------  Gag Con-Con

YVDRFYKTLRaEQAsQeV (18) [-0.88] 

        LRaEQAsQeVKNwmTETl (18) [-0.84] 

                eVKNwmTETlLVQNa (15) [-0.27] 

                     mTETlLVQNaNPDCkTIL (18) [0.07] 

                             NaNPDCkTILKALGPaA (17) [-0.05] 

                                    TILKALGPaATLeeMMTA (18) [0.66] 

                                            aATLeeMMTACQGVGGPgH (19) [0.07] 

                                                     ACQGVGGPgHKARvlAEA (18) [0.01] 

                                                             gHKARvlAEAMSqvtnsa (18) [-0.19] 

                                                                     EAMSqvtnsatiMmQr (16) [-0.22] 

                                                                           tnsatiMmQrgNfrnqrk (18) [-1.37] 

                                                                                  mQrgNfrnqrktvKCf (16) [-1.39] 

                                                                                        rnqrktvKCfnCGKeGHi (18) [-1.27] 

                                                                                                CfnCGKeGHiaknCrAPR (18) [-0.81] 

HiaknCrAPRkkGCWkcGkeGHqMkdcteRQAnFLGkIwpShkgRpgnFlQsRpEPtAPpeeSfrfgeetttpsqkqepidkelyPlaSLrsLFgnDPssq  Gag Con-B

-T-R-------------------------------------Y-----------------------S-V-----P-------------T-------------  Gag HXB2

--S----------------------------------------E------------S-------------A--------..---------K-------0R  Gag DH123

-L-r-------------------------------------s-------P----------A-i-gm---ia.SPp---qk-r-qn--v--K------lL--  Gag Con-A

---r--------------------------------------------------------a-----e-T-..-ap----k-r-..--t--k----s--L--  Gag Con-C

------------------------------------------------------------A---G----I-.------QK-------t--K-------l--  Gag Con-D

---r--------------r----------------------N------------------A---g-r--i----P---QK-eg-------K-------l--  Gag Con-F1

---R-------r------q----------------------Nr--------N--------A---G----Ia.--P---QK---Qa--i--K----S--l--  Gag Con-F2

-L-R-------------------------------------N---------N--------A---G----IA.--P----KE---------K----s--l--  Gag Con-G

---R--------------r----------------------S------------------A---G----m-.--P---lK---P.-------------l--  Gag Con-H

-----------------------------------------S------------------A--LGl---I..--P----K-------T-------S--L--  Gag Con-J

---r-------------------------------------n------------------a---G----i-.--pr--tk---qg--T--k-------l--  Gag Con-K

-l-r-------------------------------------s------------------a---gm---i-.--p---qk----------k-------l--  Gag Con-O

---r-------------------------------------s------------------a---g----i-.--p---qk----------k-------l--  Gag Con-Con

HiaknCrAPRkkGCWk (16) [-1.32] 

      rAPRkkGCWkcGkeGHqM (18) [-1.66] 

              WkcGkeGHqMkdcteRQA (18) [-1.70] 

                     HqMkdcteRQAnFLGkIw (18) [-0.98] 

                             RQAnFLGkIwpShkgR (16) [-1.14] 

                                   GkIwpShkgRpgnFlQsR (18) [-1.27] 

                                           gRpgnFlQsRpEPtA (15) [-1.21] 

                                                FlQsRpEPtAPpeeSfrf (18) [-0.98] 

                                                        tAPpeeSfrfgeetttpsqk (20) [-1.41] 

                                                                  geetttpsqkqepidkel (18) [-1.69] 

                                                                         sqkqepidkelyPlaSLr (18) [-1.01] 

                                                                                 kelyPlaSLrsLFgnDPs (18) [-0.36] All C-term AAs forbidden

                                                                                         LrsLFgnDPssq (12) [-0.75] 



Pol[Number of peptides generated: 136]

FFRedlafpqgkArefsseQtRanSptrrElqVwgrdnnSlsEAGadrqgtvSfsfPqiTLwQRPlVtikigGQlKeALLDTGADDTVleemnLPgrWKPkMiGGI  Pol Con-B

--------L-------------------------------P-------------N---V---------------------------------S-------------  Pol HXB2

----N------------------I-----------G-S--------..E--I-L-L-----------K-----------------------I----K---------  Pol DH123

----N---q--E--k------g-----S-d-wdg---s..------e----pt---------------V---------------------DI----K---------  Pol Con-A

----n------e----p----------s-----r-.--..p-----e----..ln------------s--v---i----------------i----k---------  Pol Con-C

----n--------g-l-----------S---R---g--..p--T--e-------n------------------------------------i----K---------  Pol Con-D

----N---Q--E--K-p---a-----aS---r-qrg--..p-----E-R--p-L---------------r--------------------Di----K---------  Pol Con-F1

----N---Q--E--K-----------AS---R-RrG-s..pP----E----S-L-------------a-rV----R--------------DI----K---------  Pol Con-F2

----N---Q--E--K-----------AS---R-RrG-s..pP----E----S-L-------------a-rV----R--------------DI----K---------  Pol Con-G

----N---Q-re--k--P--A------S---R-RrG-d..p-----e----.-lc-------------V--E---r---------------I----k---------  Pol Con-H

--------Q-RE---l-P---------S--PRaRRG-...PP-T--EG-----SN--------------R-----R--------------dID--rK---------  Pol Con-J

----e--s--rE--k------------s---w-r-g--..p--p-dq----p--N----------v--v-v----R---------------i----K---------  Pol Con-K

----n---q--e---------------s---rdg----..------e----s----------------v---------------------di----k---------  Pol Con-O

----n---q--e--k------------s---r-rrg--..p-----e----s-l------------------------------------di----k---------  Pol Con-Con

FFRedlafpqgkAref (16) [-0.64] 

      afpqgkArefsseQtRa (17) [-1.19] 

             refsseQtRanSptrrEl (18) [-1.81] 

                     RanSptrrElqVwgr (15) [-1.54] 

                          trrElqVwgrdnnSlsEA (18) [-1.36] 

                                  grdnnSlsEAGadrqgtv (18) [-1.22] 

                                          EAGadrqgtvSfsfPqi (17) [-0.31] 

                                                 gtvSfsfPqiTLwQRPlV (18) [0.39] 

                                                        PqiTLwQRPlVtiki (15) [0.29] 

                                                             wQRPlVtikigGQlKeAL (18) [-0.02] 

                                                                     kigGQlKeALLDTGA (15) [-0.05] 

                                                                          lKeALLDTGADDTVleem (18) [-0.10] 

                                                                                  GADDTVleemnLPgrWK (17) [-0.85] 

                                                                                         eemnLPgrWKPkMiGGI (17) [-0.68] 

rWKPkMiGGIGGFIkVrQYdqilieICGHKAiGTVLVGPTPVNIIGrnLLTQiGCTLnFPISPIeTVPVkLKPgmdGPkVKQWPLtEEKIKaLvEICtEMeKEGKiski  Pol Con-B

-------------------------------------------------------------------------------------------------------------  Pol HXB2

K--------------------V--------------------------------------------------------R------S-------T---------------  Pol DH123

K---------------k-----------K-------------------M--------------------------------------------T---------------  Pol Con-A

k---------------------p-----K-------------------m---l----------------------------------------ta--e--------t--  Pol Con-C

K--------------------------------------------------------------------------------------------t-------------r-  Pol Con-D

K---------------K---h---------------------------M--------------------------------------------T----d----------  Pol Con-F1

K---------------------p-----Q-------------------------------------------------r--------------T---------------  Pol Con-F2

K---------------------p-----Q-------------------------------------------------r--------------T---------------  Pol Con-G

k------------------e-VA-----K-------------------I--------------------------------------------T---l-----------  Pol Con-H

K------------------NEVP---E-K-------I-----------M---L--------------------------I-------------TQ--A-l-E-----R-  Pol Con-J

K--------------------vc-----q----------------------------------------------------------------r---------------  Pol Con-K

k---------------------------k-------------------m--------------------------------------------t---------------  Pol Con-O

k---------------------------k----------------------------------------------------------------t---------------  Pol Con-Con

rWKPkMiGGIGGFIkVr (17) [-0.14] 

       GGIGGFIkVrQYdqili (17) [0.41] 

              kVrQYdqilieICGHKAi (18) [-0.05] 

                      lieICGHKAiGTVLV (15) [1.45] 

                           GHKAiGTVLVGPTPVNII (18) [0.85] 

                                   LVGPTPVNIIGrnLLTQi (18) [0.72] 

                                           IIGrnLLTQiGCTLnFPI (18) [0.88] 

                                                  TQiGCTLnFPISPIeTV (17) [0.58] 

                                                         nFPISPIeTVPVkLKPgm (18) [0.16] 

                                                                 TVPVkLKPgmdGPkVKQW (18) [-0.64] 

                                                                         gmdGPkVKQWPLtEEKIK (18) [-1.16] 

                                                                                KQWPLtEEKIKaLvEI (16) [-0.39] 

                                                                                      EEKIKaLvEICtEMeK (16) [-0.42] 

                                                                                            LvEICtEMeKEGKiski (17) [-0.10] 

MeKEGKiskiGPeNPYNTPvFAIkKKdsTkWRKLVDFRELNkrTQDFWEvQLGIPHPaGLKkkkSvTvLDVGDayFSvpLdkdfRKYTaFTIPSinNetPgiRYQYNVLPQGWK  Pol Con-B

---------------------------------------------------------------------------------E--------------------------------  Pol HXB2

-------------------I------N--R-----------------------------------------------I---E------------V--AA---------------  Pol DH123

-------------------i-------------------------------------------------------------es-----------t-------------------  Pol Con-A

-------t-------------------------------------------------------------------------E--------------------------------  Pol Con-C

--------r----------I-------------------------------------------------------------e--------------------------------  Pol Con-D

----------------------------------------------------------------------------------------------v-------------------  Pol Con-F1

---------------------------------------------------------------r------------------E-------------------------------  Pol Con-F2

---------------------------------------------------------------r------------------E-------------------------------  Pol Con-G

-------------------I----------------------------------------------S-----------------------------------------------  Pol Con-H

l-E-----R-----------------------------------------------------------------------YE--------------------------------  Pol Con-J

------------------------------------------------------------------------------------------------------------------  Pol Con-K

-------------------i-------------------------------------------------------------e--------------------------------  Pol Con-O

------------------------------------------------------------------------------------------------------------------  Pol Con-Con

MeKEGKiskiGPeNPY (16) [-1.31] 

      iskiGPeNPYNTPvFAIk (18) [-0.22] 

              PYNTPvFAIkKKdsTkWR (18) [-1.19] 

                      IkKKdsTkWRKLVDFREL (18) [-1.24] 

                              WRKLVDFRELNkrTQDFW (18) [-1.33] 

                                      ELNkrTQDFWEvQLGIPH (18) [-0.95] 

                                              FWEvQLGIPHPaGLKkkk (18) [-0.54] 

                                                      PHPaGLKkkkSvTvLDV (17) [-0.32] 

                                                             kkkSvTvLDVGDayFSv (17) [0.15] 

                                                                    LDVGDayFSvpLdkdfRK (18) [-0.39] 

                                                                            SvpLdkdfRKYTaFTI (16) [-0.28] 

                                                                                  dfRKYTaFTIPSinNetPgi (20) [-0.46] 

                                                                                            PSinNetPgiRYQYNVL (17) [-0.75] 

                                                                                                   PgiRYQYNVLPQGWK (15) [-0.93] 

YQYNVLPQGWKGSPaIFqsSMTkILEPFrkqNPdivIYQYMDDLYVGSdLEIgQHRtKiEeLRqhLLrWGftTPDkKHQKePPFLWMGYELHpdKWTVQPIvLPEK  Pol Con-B

----------------------------------------------------------------------L-----------------------------------  Pol HXB2

----------------------------------------------------E-----------------LF---Q------------------------------  Pol DH123

-----------------------------sk--e-i---------------------------a---s---------------------------------e----  Pol Con-A

-----------------------------a---e----------------------A------e---k---------------------------------q----  Pol Con-C

---------------------------------E-----------------------------e-----------------------------------s-k----  Pol Con-D

------------------c----------ak--------------------------------E---k---------------------------------Q--d-  Pol Con-F1

------------------c--i-------ak--E----------------------a------E-------------------------------------Q--d-  Pol Con-F2

------------------c--i-------ak--E----------------------a------E-------------------------------------Q--d-  Pol Con-G

---------------------------------E-i--------------------a------A------------------------------------VK----  Pol Con-H

------------------C------K---ER--E------------------E---R--K---E---K---y-----------------------------Q----  Pol Con-J

------------------h----------iK--em---------------------a------e---k---------------------------------q--d-  Pol Con-K

-----------------------------tk--e----------------------a------e---k---------------------------------q----  Pol Con-O

-----------------------------ak--e----------------------a------e---k---------------------------------q----  Pol Con-Con

YQYNVLPQGWKGSPaIF (17) [-0.33] 

      PQGWKGSPaIFqsSMTkI (18) [-0.41] 

              aIFqsSMTkILEPFrk (16) [-0.07] 

                    MTkILEPFrkqNPdivIY (18) [-0.29] 

                            rkqNPdivIYQYMDDLYV (18) [-0.66] 

                                    IYQYMDDLYVGSdLEI (16) [0.01] 

                                          DLYVGSdLEIgQHRtKi (17) [-0.49] 

                                                 LEIgQHRtKiEeLRqhLL (18) [-0.76] 

                                                         KiEeLRqhLLrWGftTPDk (19) [-1.03] 

                                                                  LrWGftTPDkKHQKePPF (18) [-1.56] 

                                                                          DkKHQKePPFLWMGYELH (18) [-1.42] 

                                                                                  PFLWMGYELHpdKWTV (16) [-0.31] 

                                                                                        YELHpdKWTVQPIvLPEK (18) [-0.68] 

TVQPIvLPEKdSWTVNDIQKLVGKLnWaSQIYaGIkVkqLCKLlRGtKALTEviplTeEAELELAeNREILkepvHgvYyDPskdliaEiQKQGqGQWTYQIyQepfknLkTgKY  Pol Con-B

--------------------------------P----R-----------------------------------------------------------------------------  Pol HXB2

----------------------------------------------A--------------------------------------I-----------------------------  Pol DH123

-----e----e-----------------------------------a----DiVt-----------------d----------------------D-------------------  Pol Con-A

-----q--------------------------p----r--------a----Div----------------------------------------hd-------------------  Pol Con-C

---s-k----E---------------------p----r--------------------------------------------------------h--------------------  Pol Con-D

-----Q--d-----------------------P----r--------A----DiV---a---------------------------------------------------------  Pol Con-F1

-----Q--d-S---------------------P--Ri-H--r----a----D-V---A------------i-----------------------HD----------h--------  Pol Con-F2

-----Q--d-S---------------------P--Ri-H--r----a----D-V---A------------i-----------------------HD----------h--------  Pol Con-G

----VK--------------------------P-------------A----div---K-------------r----------------------pd-------------------  Pol Con-H

-----Q----ED--------------------P---i------i--A----DIV---R---------K--------------ArE----V----LD-------------------  Pol Con-J

-----q--d-----------------------P-------------v----diV---a------------------------------------h-----------h--------  Pol Con-K

-----q--------------------------p-------------a----div-----------------------------------------d-------------------  Pol Con-O

-----q--------------------------p-------------a----div----------------------------------------hd-------------------  Pol Con-Con

TVQPIvLPEKdSWTVNDI (18) [-0.13] 

        EKdSWTVNDIQKLVGKL (17) [-0.68] 

               NDIQKLVGKLnWaSQIYa (18) [-0.24] 

                       KLnWaSQIYaGIkVkqL (17) [-0.07] 

                              IYaGIkVkqLCKLlRGtK (18) [0.14] 

                                     kqLCKLlRGtKALTEvi (17) [0.19] 

                                            RGtKALTEviplTeEAEL (18) [-0.16] 

                                                    viplTeEAELELAeNREI (18) [-0.17] 

                                                            ELELAeNREILkepvHgv (18) [-0.47] 

                                                                    EILkepvHgvYyDPskdl (18) [-0.64] 

                                                                            gvYyDPskdliaEiQK (16) [-0.53] 

                                                                                  skdliaEiQKQGqGQWTY (18) [-1.04] 

                                                                                         iQKQGqGQWTYQIyQepf (18) [-1.29] 

                                                                                                 WTYQIyQepfknLkTgKY (18) [-1.27] 

pfknLkTgKYArmrGaHTNDvkQLtEaVQKiatesIvIWgKtPKfkLPIQkETWeawWteYwqATWIPeWEfvNTpPLVKLWYQLEkePIvgAETFYVdGAAnr  Pol Con-B

-------------------------------T-----------------------T------------------------------------------------  Pol HXB2

------------T-------------V---VT--C----------R---------T----------------------------------------------S-  Pol DH123

------------K-S---------a-v---Vvm----------------------t--md---------------------------D--a-------------  Pol Con-A

-----------K--t-----------------m------------R---------t---d------------------------------a-------------  Pol Con-C

---------------------------------------------r---------T--i-------------------------------i-------------  Pol Con-D

-----------K--S-----------------l------------r---l----dt---d--------------------------T---a----------S--  Pol Con-F1

-h----------RKS-----------V--------------i---R---------I------------------------------T---a-------------  Pol Con-F2

-h----------RKS-----------V--------------i---R---------I------------------------------T---a-------------  Pol Con-G

-----------K--s--------------------------I---r---------T----h--------0-----H---------t---a----Y---------  Pol Con-H

-----------KR-S---------aqV-----L-A----------R----r----T---D------------------------------M----------S--  Pol Con-J

-h------------S-----------v---v--------------R---------t------------------------------T-----------------  Pol Con-K

------------k-s------------------------------r---------t------------------------------------------------  Pol Con-O

--------------s------------------------------r---------t----------------------------------a-------------  Pol Con-Con

pfknLkTgKYArmrGaH (17) [-1.16] 

       gKYArmrGaHTNDvkQL (17) [-1.16] 

              GaHTNDvkQLtEaVQKia (18) [-0.46] 

                     kQLtEaVQKiatesIvIW (18) [0.24] 

                             KiatesIvIWgKtPKfkL (18) [0.11] 

                                     IWgKtPKfkLPIQkETW (17) [-0.81] 

                                            fkLPIQkETWeawWteYw (18) [-0.93] 

                                                    TWeawWteYwqATWIPeW (18) [-0.91] 

                                                            YwqATWIPeWEfvNTpPL (18) [-0.39] 

                                                                    eWEfvNTpPLVKLWYQL (17) [-0.14] 

                                                                           pPLVKLWYQLEkePIvgA (18) [0.02] 

                                                                                  YQLEkePIvgAETFYV (16) [-0.12] 

                                                                                        PIvgAETFYVdGAAnr (16) [0.11] 

TFYVdGAAnreTklgKAGYVTdrGRQkVvsltDTTNQKTELqAIhLALQDSGlEVNIVtDSQYAlGIIqAQPDkSESElVsqIIEqLIkKekVYLaWVPAHKGIGGNEqv  Pol Con-B

---------------------N-------T--------------Y----------------------------Q------N-----------------------------  Pol HXB2

--------S---R--------N----------------------Y-----------------------------------N-----------------------------  Pol DH123

--------------------------------e--------h----------S--------------------r------N----K--g-d----s--------------  Pol Con-A

-------------i-------------i----E-----------q-------s---------------------------n----------r---S--------------  Pol Con-C

-----------------------------pf-------------N-----------------------------------------------------------------  Pol Con-D

-------S-----K-------------a----E-----A-------------S-------------------------i-N-------q--r---S--------------  Pol Con-F1

-------------------i---------p--E-------------------S-----------------h-------i-N-------Q--r---S--------------  Pol Con-F2

-------------------i---------p--E-------------------S-----------------h-------i-N-------Q--r---S--------------  Pol Con-G

Y-----------i----------K-------E-----------Y-----------------------------------N----E---------S---------------  Pol Con-H

-------S-----t--------K-----iT-----------h--Y-------i---------------------------N----E---------S--------------  Pol Con-J

-------------q----------------I-e-----a-------------s---------------------------n----------R---S--------------  Pol Con-K

--------------------------------e--------h----------s--------------------r------n--------------s--------------  Pol Con-O

--------------------------------e-------------------s---------------------------n--------------s--------------  Pol Con-Con

TFYVdGAAnreTklgKA (17) [-0.59] 

       AnreTklgKAGYVTdrGR (18) [-1.34] 

               KAGYVTdrGRQkVvsl (16) [-0.58] 

                     drGRQkVvsltDTTNQK (17) [-1.49] 

                            vsltDTTNQKTELqAIhL (18) [-0.35] 

                                   NQKTELqAIhLALQDSGl (18) [-0.37] 

                                           IhLALQDSGlEVNIV (15) [0.81] 

                                               LQDSGlEVNIVtDSQYAl (18) [0.06] 

                                                       NIVtDSQYAlGIIqA (15) [0.53] 

                                                            SQYAlGIIqAQPDkSESEl (19) [-0.55] 

                                                                     AQPDkSESElVsqIIEqL (18) [-0.54] 

                                                                             ElVsqIIEqLIkKekVYL (18) [0.11] 

                                                                                    EqLIkKekVYLaWVPAHK (18) [-0.50] 

                                                                                            VYLaWVPAHKGIGGNEqv (18) [0.11] 

HKGIGGNEqvDkLVSaGiRkVLFldGIdkAQeeHEkYHsNWrAMAsdFNlPpvvAKeIVAsCdKCQlKGEAmHGQVDcSPGIWqLDCTHLegkiILVAVHVASGYIeAEVIPa  Pol Con-B

-------------------------------D-------------------------------------------------------------V-------------------  Pol HXB2

---------------T---R-------E------------------E----A--------C-----V--------------------------V-------------------  Pol DH123

---------------s-------------------r------t---------i----------------------------------------V-------------------  Pol Con-A

---------------s------------------------------e-----i------------------------------------------------------------  Pol Con-C

---------------q----------------------n------------------------------------------------------v-------------------  Pol Con-D

--------------------i-----------------N--------------------------------------------------------------------------  Pol Con-F1

---------------s-------------------------------------------------------------------------------------------------  Pol Con-F2

---------------s-------------------------------------------------------------------------------------------------  Pol Con-G

--------------S----------------q--r--n-------------I----------------------------------------v--------------------  Pol Con-H

---------------S----------------d------------------------------------------------------------V-------------------  Pol Con-J

---------------s----------------------n-------------i------------------i-----------------------------------------  Pol Con-K

---------------s-------------------r----------------i------------------------------------------------------------  Pol Con-O

---------------s-------------------------------------------------------------------------------------------------  Pol Con-Con

HKGIGGNEqvDkLVSaGi (18) [-0.24] 

       EqvDkLVSaGiRkVLFl (17) [0.54] 

              SaGiRkVLFldGIdkA (16) [0.39] 

                    VLFldGIdkAQeeHEkYH (18) [-0.89] 

                            kAQeeHEkYHsNWrAMA (17) [-1.88] 

                                   kYHsNWrAMAsdFNlPpv (18) [-0.71] 

                                           MAsdFNlPpvvAKeIVA (17) [0.74] 

                                                  PpvvAKeIVAsCdKCQlK (18) [0.18] 

                                                          VAsCdKCQlKGEAmHGQV (18) [-0.22] 

                                                                  lKGEAmHGQVDcSPGIW (17) [-0.20] 

                                                                         GQVDcSPGIWqLDCTHL (17) [-0.04] 

                                                                                GIWqLDCTHLegkiILVA (18) [0.74] 

                                                                                        HLegkiILVAVHVASGYI (18) [1.14] 

                                                                                                VAVHVASGYIeAEVIPa (17) [1.10] 

GYIeAEVIPaeTgQeTAYFlLkLAgRWPVktiHTDNGsNFtsttVkAAcWWaGikQeFGiPYNPQSQGVveSmnkeLKkIIgQVRDQAEHLKtAVqMAVFIHNfkRK  Pol Con-B

-----------------------------------------GA--R-------------------------------------------------------------  Pol HXB2

-------------------I-------------------------------------------------------------E-------------------------  Pol DH123

------------------------------vv----------AA--------nvq------------------------------E---------------------  Pol Con-A

-------------------i----------v-----------aa----------Q----------------------------------------------------  Pol Con-C

------------------------------vV----------Aa---------------------------------------------------------------  Pol Con-D

-------------------i----------i-----------aa----------Q----------------------------------------------------  Pol Con-F1

---------------a---I----------I-----------aV----------Q----------------------------i-----------------------  Pol Con-F2

---------------a---I----------I-----------aV----------Q----------------------------i-----------------------  Pol Con-G

------------------i----------m-----------aA--------D-q------------------------------------r----------------  Pol Con-H

---------------A-F-I----------a-----------GA--------D--------------------------------E---------------------  Pol Con-J

-------------------I----------V-----------av--------d------------------------------------------------------  Pol Con-K

-------------------i----------v-----------aa--------n-q----------------------------------------------------  Pol Con-O

-------------------i----------v-----------aa----------q----------------------------------------------------  Pol Con-Con

GYIeAEVIPaeTgQeTAY (18) [-0.29] 

        PaeTgQeTAYFlLkLAgR (18) [-0.24] 

                AYFlLkLAgRWPVktiH (17) [0.36] 

                       AgRWPVktiHTDNGsNF (17) [-0.84] 

                              tiHTDNGsNFtsttVkAA (18) [-0.44] 

                                      NFtsttVkAAcWWaGik (17) [0.18] 

                                             kAAcWWaGikQeFGiPY (17) [-0.04] 

                                                    GikQeFGiPYNPQSQGVv (18) [-0.43] 

                                                            PYNPQSQGVveSmnkeLK (18) [-1.18] 

                                                                    VveSmnkeLKkIIgQVR (17) [-0.24] 

                                                                           eLKkIIgQVRDQAEHLK (17) [-0.86] 

                                                                                 gQVRDQAEHLKtAVqMAV (18) [-0.36] 

                                                                                         HLKtAVqMAVFIHNfkRK (18) [-0.14] 

AVFIHNfkRKGGIGgYsAGeRIvdiIAtDiQtkeLQkQiTkiQnfRVYYRdsrdPlWKGpAKLLWKGEGAVVIQDnsdIKVVPRRKaKiIRDYGKQmagDDCVAsRQDED  Pol Con-B

-----------------------------------------------------N--------------------------------------------------------  Pol HXB2

---------------------------S-----------------------------------------------K----------------------------------  Pol DH123

----------------------I--------------------------------i------------------------------------------------g-----  Pol Con-A

----------------------i----------------i---------------i----------------------------------k--------A----g-----  Pol Con-C

----------------------I----------------i---------------i------------------------------v-----------------------  Pol Con-D

----------------------I---------r------i---------------V---------------------E--------------------------G-----  Pol Con-F1

----------------------I----------------s--------F------V--------------------NE---i----------------------G-----  Pol Con-F2

----------------------I----------------s--------F------V--------------------NE---i----------------------G-----  Pol Con-G

---------------------I----------------Sn--K-----------I---------------------E--------------------------g-----  Pol Con-H

----------------------I---------r----------------------I-------p-------------E--------------------------G-----  Pol Con-J

----------------------i----------------l-------------e-I---------------------e--------------------------g-----  Pol Con-K

----------------------i--------------------------------i------------------------------------------------g-----  Pol Con-O

----------------------i--------------------------------i---------------------e--------------------------g-----  Pol Con-Con

AVFIHNfkRKGGIGgYsA (18) [-0.02] 

        RKGGIGgYsAGeRIvdiI (18) [-0.00] 

                sAGeRIvdiIAtDiQtk (17) [0.05] 

                       diIAtDiQtkeLQkQiTk (18) [-0.62] 

                               tkeLQkQiTkiQnfRVYY (18) [-0.99] 

                                       TkiQnfRVYYRdsrdPlW (18) [-1.26] 

                                               YYRdsrdPlWKGpAKLLW (18) [-1.08] 

                                                       lWKGpAKLLWKGEGAVVI (18) [0.45] 

                                                               LWKGEGAVVIQDnsdIKV (18) [-0.03] 

                                                                       VIQDnsdIKVVPRRKaKi (18) [-0.51] 

                                                                               KVVPRRKaKiIRDYGKQm (18) [-1.02] 

                                                                                       KiIRDYGKQmagDDCVA (17) [-0.42] 

                                                                                              KQmagDDCVAsRQDED (16) [-1.37] 



Vif[Number of peptides generated: 25]

menrwqvmiVWQvDRmrIrtwksLVkhHmyisgkakgwfyrhHyesthPrissevhIPlgdarlvitTywGlhtgerdWhlgqgvsiewrkkrYstqvdpdl  Vif Con-B

------------------------------V----R----------P-----------------------------------------------------E-  Vif HXB2

------------------------------V-K-----------------------------S--V-------------------------R----------  Vif DH123

---------------------n--------v-k-------------R--kv--------------vr---------k-----h-------lr-----i----  Vif Con-A

-------L--------k----n--------v-rr-n----------R--kv---------e-----k-----q---------H-------lr--------G-  Vif Con-C

------------------------------v-k--q--l-----dcp--K----------e----vk----------e-------------r--------G-  Vif Con-D

------------------n-------Y--hv-K----------Fq-R--k---------Ee-k----------p----------------QG--R--I--g-  Vif Con-F1

---------------------N----------rR-a----------R---V--------E-DSK--I---------------h-------Q---R-------  Vif Con-F2

---------------------n--------v-K-------------R---V-----------k--Vr---------K--q--H-------Qr-----i----  Vif Con-G

------------------n-------y--nv-k--rk-l-----d----k----------e-----------q-----------------q---r-----g-  Vif Con-H

------------------n-------y---v-K--nr-y-------h--K------------e--v-----------s------------L-k-r-------  Vif Con-K

---------------------n----y---v-k-------------r---v---------e----v------m---------h-------y-k----i----  Vif Con-O

------------------------------v-k-------------r--k---------------v------------------------q-----------  Vif Con-Con

menrwqvmiVWQvDRmrI (18) [-0.31] 

        iVWQvDRmrIrtwksLVk (18) [-0.24] 

                rIrtwksLVkhHmyisgk (18) [-0.73] 

                        VkhHmyisgkakgwfyrh (18) [-0.87] 

                                gkakgwfyrhHyesthPr (18) [-1.82] 

                                        rhHyesthPrissevhI (17) [-1.27] 

                                               hPrissevhIPlgdarlv (18) [-0.04] 

                                                       hIPlgdarlvitTywGlh (18) [0.33] 

                                                               lvitTywGlhtgerdWhl (18) [-0.21] 

                                                                       lhtgerdWhlgqgvsiew (18) [-0.73] 

                                                                               hlgqgvsiewrkkrY (15) [-1.22] 

                                                                                    vsiewrkkrYstqvdpdl (18) [-1.12] 

rYstqvdpdladqLIHlyyfdCfsesAirnailghivsprCeyqaGHnkvgslqYLALaalitpkkikPPlPsvtkltEDRWNkpqktkghrgshtmngh  Vif Con-B

--------E---------------D----K-L--------------------------------------------------------------------  Vif HXB2

-----------------------------------R-------------------------V--R---------A---------SH--------------  Vif DH123

-----i-----------h------d----k----qv---s------------------k--v------------r-------------r----------c  Vif Con-A

--------G-------mh-----ad----k-------i---d----------------T---K-----------r--V----------R-r--n------  Vif Con-C

--------G-------m------a-----k-------t---n----------------t---a-----------r-----------r-------------  Vif Con-D

--R--I--g-------I------------K-----rI----n----------------T---a---t-------q--V--------e-R-----------  Vif Con-F1

--R--------------h------d----k-----R-----N----------------T---------------R--V-----N----r-----------  Vif Con-F2

-----i------h----h-----------k----q--r-----p--------------K--V--tr-r------r-------------R---enp-----  Vif Con-G

--r-----g-------mh------d----k----q------d----------------T---a--rr-------q--V----------r---e-------  Vif Con-H

k-r-------------i------------k-----r-----------kq---------T--va---p---v---q--v----------r-----------  Vif Con-K

k----i-----------h-----------k----qr----------------------r--vk--rt-------q-------------r-----------  Vif Con-O

-----------------h-----------k----------------------------t---a-----------q--v----------r-----------  Vif Con-Con

rYstqvdpdladqLIHly (18) [-0.50] 

        dladqLIHlyyfdCf (15) [0.40] 

             LIHlyyfdCfsesAirna (18) [0.33] 

                     CfsesAirnailghiv (16) [0.86] 

                           irnailghivsprCeyqa (18) [0.04] 

                                   ivsprCeyqaGHnkvgsl (18) [-0.36] 

                                          yqaGHnkvgslqYLALaa (18) [0.06] 

                                                  gslqYLALaalitpkkik (18) [0.53] 

                                                          aalitpkkikPPlPsvtk (18) [0.01] 

                                                                  ikPPlPsvtkltEDRWNk (18) [-1.02] 

                                                                          tkltEDRWNkpqktkghr (18) [-2.39] 

                                                                                  Nkpqktkghrgshtmngh (18) [-2.19] 

                                                                                          hrgshtmngh (10) [-1.8] 



Vpr[Number of peptides generated: 12]

MeqaPedqGpqrepyneWtLelleeLknEAvrhFpriWLhsLgqhiYetYGdtWaGveaiiRiLQQlLfihFRigCqHSRigitqqrrarngasrs  Vpr Con-B

--------------H-------------------------G-----------------------------------R-----V-R-----------  Vpr HXB2

---V-Q------------------------------P---G---Y-----------------------L--------------IR---T-------  Vpr DH123

------------------m-----d--h--------p---G------n------E-------t------v-------------irg--v-d-sg--  Vpr Con-A

---------------------------q--------P---g---y---------t----l-----------------------lr-----------  Vpr Con-C

---------------------------S----------------y---------------------------------------r-------s---  Vpr Con-D

-----g------------a-----------------P---g------N------E---------------------r------ir---V-------  Vpr Con-F1

---P-----------------------h--------Ey--G------N------r---------------------H------IR---i---S---  Vpr Con-F2

------------------a-----------------p---G------N------E-----------------------------pr--v-d-pg--  Vpr Con-G

--------------H--0--------s--------p---q------N------e----l--T---------------------R---V---P---  Vpr Con-H

-------h-------H--------------------P-------Y--S------E---------------------H------IP---G-------  Vpr Con-J

---------------------i-----r--------p---d------n------E---------------------h------ip---g-------  Vpr Con-K

---------------------------a--------p---g---y---------e--------------v-------------nrr--g-------  Vpr Con-O

------------------------------------p---g------n------e----------------------------ir---v-------  Vpr Con-Con

MeqaPedqGpqrepyneW (18) [-2.21] 

        GpqrepyneWtLelleeL (18) [-1.13] 

                eWtLelleeLknEAvrhF (18) [-0.57] 

                        eLknEAvrhFpriWLhsL (18) [-0.47] 

                                hFpriWLhsLgqhiYetY (18) [-0.48] 

                                        sLgqhiYetYGdtWaGv (17) [-0.37] 

                                               etYGdtWaGveaiiRiL (17) [0.34] 

                                                      aGveaiiRiLQQlLfihF (18) [1.34] 

                                                              iLQQlLfihFRigCqHSR (18) [0.33] 

                                                                      hFRigCqHSRigitqqrr (18) [-1.02] 

                                                                              SRigitqqrrarngasr (17) [-1.38] 

                                                                                     qrrarngasrs (11) [-2.13] 



Vpu[Number of peptides generated: 9]

mqslqilaivalvvaaiiaIvVwsivfieyrkilrQrkidrlidrireraedsGNeSegdqeelsalvemGhhapwdvddl  Vpu Con-B

T-PIP-V--------I----------I------------------LI------------...-I-----------------  Vpu HXB2

--P-V----------L--V-------L---------K--------------------D-----------R--L----I---  Vpu DH123

-sp-e-w---g-i--l-l-----T--g---k-l-k--------e-------------d--t------i---nYdLG-dNn-  Vpu Con-A

akvdyr-gvg--i--l-------t-aY-----l-------w--k----------------t----tm-d---LRLL--n--  Vpu Con-C

--p-v----------l-------t-----c-rlk------w-------------------r-------------------m  Vpu Con-D

-Sn-laig-a--I--L-------T--y---K-Lv-----N--Yk----------------A---A--G---pFI-G-iNN-  Vpu Con-F1

-p-sLaVv-a-yI--L----I--T--Y---K-----KR-N--YE--i-------------A---A--G-V-PlI-G-INN-  Vpu Con-F2

--p-e-s---g-I--f-A--i--t-------e-Rk-k--ek-l-----------------t---at-m---dFD--VG-N-  Vpu Con-G

-yi-G-.G-G-----F-------T--Y-----Lvk-k------e--i----------D--t----k------LnlGY-A--  Vpu Con-H

-ip---a-----I--iFL--cm-T--Y---K-L-------K----------------D--Td--Ad---r-P-DL-N-N--  Vpu Con-J

-v--isg.-i---a-l-l--I--t-aY------v--kr-nw-------------------a---a-ig-t--liLgsisn-  Vpu Con-K

--p-e-----g-i--l-------t--l------kk-------l-----------------t----t-------d-----n-  Vpu Con-O

--p---------i--l-------t--y---------k-----------------------t-----------ld-----n-  Vpu Con-Con

mqslqilaivalvvaaii (18) [2.41] 

        ivalvvaaiiaIvVwsiv (18) [3.17] 

                iiaIvVwsivfieyrkil (18) [1.84] 

                        ivfieyrkilrQrkidrl (18) [-0.28] 

                                ilrQrkidrlidrirera (18) [-0.97] 

                                        rlidrireraedsGNeSe (18) [-1.66] All C-term AAs forbidden

                                                raedsGNeSegdqeelsa (18) [-1.77] 

                                                        SegdqeelsalvemGhha (18) [-0.69] 

                                                                salvemGhhapwdvddl (17) [-0.15] 



Tat[Number of peptides generated: 13]

MepVdprLEPWkHPGSQPktactnCyCKkCCfHCqvCFttkgLgIsyGrKKRrqRRrapqdsqthQvsLskQpasqprGDptgpkeskkkVerEtEtdpvdq  Tat Con-B

--------------------------------------I--A----------------H-N-----A------T------------0-----------F-  Tat HXB2

-------------------------------L------I--------------K---S--H---D-A-------------------------T-------H  Tat DH123

-d----n----n------t-p-nk-------y------ln----------------gt--s-kd--npip---ip-tq-is---e-------ska---rf-  Tat Con-A

------n----n----------nk------sY--l---q-----------------s--ps-ed--nli----Lprtq-----se-------sK-----f-  Tat Con-C

-d----n----N------r-p-Nk-------Y------i------------------p--gg-a--dpiP---S------------  Tat Con-D

--l---n-D--N------t-P--k----r-----yw--a----------------h-T--S--i--dpvP---l--a------------E--SKak---c-  Tat Con-F1

--V---kiD---------E-P-Nk----------pL---r-----------------T--s-ki--DPVp---L--T----k--E-------SQ-----  Tat Con-F2

-D----k----n--------p-Nk----v--w------LN------------kh--gt--s-Kd--nPVP---lptT--N---------e-aSK-----f-  Tat Con-G

-D----nq---N------q---N--------y---l--LK------------s---aT-aSl-D--nhIp---L-RTh--------  Tat Con-H

------NR---N-------------------Y------LQ----------------S--PG-K---DLIP---L--TQRK----E----E--SKA-P-RF-  Tat Con-J

------ni---Nq---------Nq----r--Y---i--lk----------------tT-ya-kn--Dpip---L------q--------a--SK-K---  Tat Con-K

------n----n------t---nk-------y------lk----------------gt--s-kd--npip---lp-t------------e--ska----f-w  Tat Con-O

------n----n----------nk-------y------l------------------t--s-kd--dpip---l--t---------------sk-----f-w  Tat Con-Con

MepVdprLEPWkHPGSQPk (19) [-1.56] 

         PWkHPGSQPktactnCy (17) [-1.22] 

               SQPktactnCyCKkCCfH (18) [-0.55] 

                       nCyCKkCCfHCqvCFttk (18) [0.01] 

                               fHCqvCFttkgLgIsyGr (18) [0.18] 

                                       tkgLgIsyGrKKRrqRRr (18) [-2.11] 

                                               GrKKRrqRRrapqdsqth (18) [-2.98] 

                                                       RrapqdsqthQvsLsk (16) [-1.56] 

                                                             sqthQvsLskQpasqpr (17) [-1.35] 

                                                                    LskQpasqprGDptgpk (17) [-1.57] 

                                                                          sqprGDptgpkeskkkV (17) [-2.02] 

                                                                                 tgpkeskkkVerEtEtdpv (19) [-1.88] 

                                                                                          VerEtEtdpvdq (12) [-1.68] 



Rev[Number of peptides generated: 15]

MAgRsgdSdEeLlktvrlikflYqSNppPspeGTrqARRNRRRRWreRQRqirsiSgwilstyLGrpaepVplqLPPlerLtLdcneDCGtsGtqGvGspqilv  Rev Con-B

------------IR------L--------N----------------------H---ER--G-----S-------------------------------------  Rev HXB2

------E---D--N------L------L--L---------------Q-----Q--------NH-----DA----------------------------T-----  Rev DH123

-------------rAi-i--i------y-k-k-s----K-------A-----D-l-eR----C------------------h---s------------r--vs-  Rev Con-A

----------a--qA--i--i------Y-e--------k-------A-----h---eR----c--------------i---hi--S-sg-----------0sGk  Rev Con-C

----------d---A-----i-------------------------A-----h--gER--------se-------------n-N-s----------------s-  Rev Con-D

---------t----A--y--I------Y-k----------------A------a--dR---sC----e-------------HIN-S----.....-------Sg  Rev Con-F1

-------r------A--Y--I------Y-K----------------A-----Hq--ER---------q---r---------hIN-S----.....-------S-  Rev Con-F2

------st-----ra--i--i------y-p----------------A-----h---ER---ac------------------h---S--g---------r---f-  Rev Con-G

------a---q--qvCkI--i------y-E-a--------------A------a--ER--tsC----p-----------------s-------..-k-----sl  Rev Con-H

---------DQ--LA--i--I------Y-K-N-S------------A--N--D---ER-p-SC--------------I---R---S----N---.---D---SG  Rev Con-J

----R--p-qQ--Tp--i--I------Y-k---s------------A---------qRl--aC---S----------i---s-N-D--p-kq--.eL-----p-  Rev Con-K

-------------ra--i--i------y-k--------k-------a-----h---er----c---s--------------h---s--------.-------s-  Rev Con-O

--------------a--i--i------y-k----------------a-----h---er----c------------------h---s--------.-------s-  Rev Con-Con

MAgRsgdSdEeLlktvrl (18) [-0.59] 

        dEeLlktvrlikflY (15) [0.13] 

             ktvrlikflYqSNppPs (17) [-0.51] All C-term AAs forbidden and proline at position 18

                    flYqSNppPspeGTrqAR (18) [-1.39] 

                            PspeGTrqARRNRRRRWr (18) [-2.82] 

                                    ARRNRRRRWreRQRqir (17) [-3.15] 

                                           RWreRQRqirsiSgwil (17) [-1.15] 

                                                 RqirsiSgwilstyLGr (17) [-0.12] 

                                                        gwilstyLGrpaepVpl (17) [0.27] 

                                                               LGrpaepVplqLPPlerL (18) [-0.16] 

                                                                       plqLPPlerLtLdcneDC (18) [-0.39] All C-term AAs forbidden

                                                                               rLtLdcneDCGtsGtqGv (18) [-0.52] 

                                                                                       DCGtsGtqGvGspqilv (17) [0.15] 

tqGvGspqilvEsPavLesGtkEe  Rev Con-B

--------------T--------  Rev HXB2

-----T-----------------  Rev DH123

-----r--vs----v--g----n  Rev Con-A

-------0sGk-c---g--a-K-  Rev Con-C

---------s-------d---e-q  Rev Con-D

..-------Sg--ht--------  Rev Con-F1

..-------S---h-a-G--i--  Rev Con-F2

-----r---f---sV--G-----  Rev Con-G

..-k-----sl--st--GT----  Rev Con-H

-.---D---SG-PCM--GA----  Rev Con-J

-.eL-----p--PcT-----d--  Rev Con-K

-.-------s-----i-g-----  Rev Con-O

-.-------s-------g-----  Rev Con-Con

tqGvGspqilvEsPavL (17) [0.57] 

       qilvEsPavLesGtkEe (17) [-0.20] 



Env[Number of peptides generated: 114]

MrvkgirknyqhlwrwGtmllGmlmicsaaeqlwVTvYYGVPVwkEatTTLFcASdAkaydtevHNvWAthACvPTdPnpqevvlenVTenfnmwkNnmveqMh  Env Con-B

---EKYQHLWRWG----------------T-K-----------------------------------------------------V-----------D------  Env HXB2

---M----------KG--L---I------------------------N----------------------------------IL------D-------------  Env DH123

---m--qr-c---l-----i---ii------n-------------d-e----------------------------------ih------e-------------  Env Con-A

---m--qr-c-qW-i--iLGFW-----nvmgn---------------k------------e---------------------m--------------d--d---  Env Con-C

---r--qr------k--i----i--t----dn--------------------------s-e--a--i---------------ie--------------------  Env Con-D

---R-MQR-W---GK--LLF--i-I--n--dn--------------------------s-Er-a-------------------a-k------d-----------  Env Con-F1

---REMQR-W---G---LLF--I-I--as-aD--------------p--------------p--------Y-------s---L--G--s-k---------D---  Env Con-F2

------qR-w--------Li--lvi----snn------------ed-d------------s--k------------------i---------------------  Env Con-G

---.retQr-W-t-g---ilf--i-i------n.----------------------------s----------------------s-p--------------d-  Env Con-J

---r-mQr-W---gkr-iLf--i-I-----d-----------------------------e----------------------l--------------------  Env Con-K

---retQr-W-t-g---ilf--i-i------n----------------------------s----------------------s-p--------------d---  Env Con-J

---r--qr-w-------ilf--i-i------n----------------------------e-------------------------------------------  Env Con-Con

Mrvkgirknyqhlwrw (16) [-1.29] 

      rknyqhlwrwGtmllGml (18) [-0.48] 

              rwGtmllGmlmicsaa (16) [1.25] 

                    lGmlmicsaaeqlwVTvY (18) [1.28] 

                            aaeqlwVTvYYGVPVwk (17) [0.36] 

                                   TvYYGVPVwkEatTTLF (17) [0.31] 

                                          VwkEatTTLFcASdAkay (18) [0.03] 

                                                  LFcASdAkaydtevHNvW (18) [-0.11] 

                                                          aydtevHNvWAthACv (16) [0.00] 

                                                                HNvWAthACvPTdPnpqev (19) [-0.65] 

                                                                         vPTdPnpqevvlenV (15) [-0.39] 

                                                                              npqevvlenVTenfnmwk (18) [-0.78] 

                                                                                      nVTenfnmwkNnmveqMh (18) [-1.10] 

wkNnmveqMhediIsLWdqsLKPcVkltPLCvtLnctdlnnntnttsssgekmekgeiknCSfnittsirdkvqkeyalfykldvvpidndntsyrlisCntSvitQACPkv  Env Con-B

---D----------------------------S-K----K-D---N----RM-------------S----G-------F-----II-----.-T-K-T--------------  Env HXB2

----------------------------------H----K-G--LKGTKIIG-.R---------V-KN-I---K-------RH------RN.IT---------TL-------  Env DH123

----------t-------------------------snv-ttnt-n-.....-.re--------m--El---k--v-s---r----q-e-nssq----N----a--------  Env Con-A

---d--d------------------------------nv-tts--n...mg....------------el---k--v-----r--i--le-nsse----n----a--------  Env Con-C

--------------------------------------asr-st-nn.....e-p-am---------ev---k-qvh----r--i-----ns-n----n----a--------  Env Con-D

----------t--------------------------natttsqa-i--tl-E-p-A-Q-----m--Ev---kl-vh----r--I---n-ssse----n----T--------  Env Con-F1

------D---l---------------s----------kaiItmssstlapl-tiqe-----------E----qr-qq----r---e--.kNSst---------Tl-------  Env Con-F2

------------------e------------------nv---nt-nt.....t-ia-----------e----kk-------r-------dn.sn----n--v-t-k------  Env Con-G

--------d---t-------e-------------------vt..s-..nsdtnsnatvispd-----------E-k--kKq------r------..-sesnke.----N---  Env Con-J

----------t-------e---------------t---yygtrrnatniratsp.a-----------Elk--KKqvs----r--------nssn----N----tv-------  Env Con-K

------d---t-------e-------------------vt..s-..dtnsnaispd-----------E-k--kKq------r------.-sesn----N----t--------  Env Con-J

----------t--------------------------nv-ttst-n----l---p------------e----k--v-----r--------nssn----n----t--------  Env Con-Con

wkNnmveqMhediIsLW (17) [-0.58] 

      eqMhediIsLWdqsLK (16) [-0.76] 

            iIsLWdqsLKPcVkltPL (18) [0.54] 

                    LKPcVkltPLCvtLnctdl (19) [0.78] 

                             LCvtLnctdlnnntntts (18) [-0.26] All C-term AAs forbidden

                                     dlnnntnttsssgekmek (18) [-1.75] 

                                             tsssgekmekgeiknCSf (18) [-1.04] 

                                                     ekgeiknCSfnittsir (17) [-0.64] 

                                                            CSfnittsirdkvqkeya (18) [-0.57] 

                                                                    irdkvqkeyalfykldvv (18) [-0.19] 

                                                                            yalfykldvvpidndntsy (19) [-0.17] 

                                                                                     vpidndntsyrlisCntSv (19) [-0.26] 

                                                                                              yrlisCntSvitQACPkv (18) [0.37] 

SvitQACPkvsfePIpihycapagfailkCndkkFngtgpCtnVStvqCtHGirPvvSTqlLlngSlaeeevvirsenftdnaktIivqLnesveinctrpnnntrksihi  Env Con-B

-------------------------------N-T------------------------------------------V--------------T---------------R-R-  Env HXB2

-TL---------------------------K---------------------------------------------S-------I-------T--------------G-TL  Env DH123

-a-------------------------------e-------k-----------k------------------m-----i-n---------tkp-k--------------r-  Env Con-A

-a----------d-----------y------n-t-------n-----------K-----------------ii-----l-n-------h-------v------------r-  Env Con-C

-a----------------------------r----------k-----------------------------ii-----l-n-------h-----q------y----qrtp-  Env Con-D

-T---------WD-----------Y--------r-------k----------------------------gIi---Q-iS--------H-----Q---------------l  Env Con-F1

-Tl---------D-----------y--------r-------rk-------------------------q-kiI---k-Is--T------Fkrp-i-d-r-------r----  Env Con-F2

-t-k--------d-----------------r--n-------k-----------k-----------------ii-----i---t-v-------ti-----------------  Env Con-G

e.----N----t-------------------------------t-------k-----------K-----------------Ii-----is--t-N-------t--------  Env Con-J

-tv------------------------------r-------------------K-----------------Ii----si-k-t-N-------t-p------s---------  Env Con-K

-t-------------------------------t-------k-----------K-----------------Ii-----is--t-N-------t-----------------m  Env Con-J

-t-------------------------------r-------k-----------k-----------------ii-----i--------------------------------  Env Con-Con

SvitQACPkvsfePIpih (18) [0.43] 

        kvsfePIpihycapagfa (18) [0.49] 

                ihycapagfailkCndkk (18) [0.04] 

                        failkCndkkFngtgpCtnV (20) [-0.23] 

                                  FngtgpCtnVStvqCtH (17) [-0.21] 

                                         tnVStvqCtHGirPvv (16) [0.26] 

                                              vqCtHGirPvvSTqlLl (17) [0.71] 

                                                     rPvvSTqlLlngSla (15) [0.64] 

                                                          TqlLlngSlaeeevvir (17) [0.35] 

                                                                 Slaeeevvirsenftdna (18) [-0.46] 

                                                                         irsenftdnaktIivqL (17) [-0.12] 

                                                                                dnaktIivqLnesvei (16) [0.07] 

                                                                                      ivqLnesveinctrpnnntr (20) [-0.86] 

                                                                                                nctrpnnntrksihi (15) [-1.49] 

nnntrksihigpgrafyttgeiigdirqAhCnisrakwnntLkqiviklreqfgnktIvFnqssGGDpeivmhsfnCgGEffyCnttqLFnstwnstntegsnntdti  Env Con-B

------R-R-QR-GRAFV-IGK--NM-------------------AS-----------I-K----------T-------------S-----------WSTEGS-S---  Env HXB2

------G-TL----V-------V----K------KV--H----RV-E----K-E-------K------------------------KK------...-GTEGSYN---  Env DH123

--------r----q---a--d-----------v--se--k--qkvakq--ty-n.---i-tn-----l--TT--------------sg----------dqe--s----  Env Con-A

--------r----Qt--a--d-------------gt---e--qrVsk--a-h-p----k-ap-----l--tt-----r--------sk-----y---.......ns--  Env Con-C

y----qrtp--l-q-l---rs-------------g-q--k--q-Var--gnlln-t--i-kp--------tt--------------sg---------......sng--  Env Con-D

---------l---q---a---------K------GtQ--k--ayVka--ksh-p----k--------L--T------r------d-sg---d-...........nG--  Env Con-F1

-----r-------q---A---------K-------kq-yd--ik-atEFKkhy.--sVa-qp-a---l--TT-----R-----y--si---h-r..Vadit-htN---  Env Con-F2

-------------q---a--d-----------v-gt---em-qkvkaq-gki-n----t--s-a---l--tt-----r--------sg----s-t-........N---  Env Con-G

-t-----------------m---.q---a--d-------------ged-----rrvkk----h-.-.---i-tpp-------tt-----r--------sk------..  Env Con-J

s----------------a--d-------------geq--p--nrvkee-kkh-k-i--i-qppn-----vth-m---r---------k---.............dt--  Env Con-K

---------m---q---a--d-------------ged-----rrvkk----h-.----i-tpp-------tt-----r--------sk------..........nt--  Env Con-J

-------------q---a--d-------------geq--k--qrvkk----h-n----i--p-----l--tt-----r--------sg---------.......n---  Env Con-Con

nnntrksihigpgrafy (17) [-1.07] 

       ihigpgrafyttgeii (16) [0.37] 

             rafyttgeiigdirqAh (17) [-0.37] 

                    eiigdirqAhCnisrakw (18) [-0.45] 

                            AhCnisrakwnntLkqiv (18) [-0.49] 

                                    kwnntLkqiviklreqf (17) [-0.69] 

                                          kqiviklreqfgnktIvF (18) [0.00] 

                                                  eqfgnktIvFnqssGGDpei (20) [-0.74] 

                                                            nqssGGDpeivmhsf (15) [-0.57] 

                                                                 GDpeivmhsfnCgGEffy (18) [-0.03] 

                                                                         sfnCgGEffyCnttqLF (17) [0.10] 

                                                                                ffyCnttqLFnstwnstn (18) [-0.52] All C-term AAs forbidden

                                                                                        LFnstwnstntegsnntdti (20) [-1.03] 

tegsnntdtitlpCrIkqiiNmwQeVgkamYApPirGqirCsSnITGllLtrdggnnnntteiFrpgggdmrdnwrseLykYKvvkieplgvAPTkakRRvvqrEkrav  Env Con-B

STEGS-S-----------------K----------S--------------------S--ES------------------------------------------------  Env HXB2

GTEGSYN----------------------------S---W---------------K.-SS-------------------------RV----I-----------------  Env DH123

dqe--s------------------ra-q-------q-v---e----------------s-n-t---------------------------------------e------  Env Con-A

......ns----------------g--r-------a-n-t-k-------------ttt----t----------------------e-k--------------e------  Env Con-C

.....sng----------------g----------e-n-n---------------i--s-n-T--------------------------------r------e-----i  Env Con-D

......nG-----------v-------r----a--A-n-t-N-------------.qssri-T---e--n-K-------------E-------------q-----r---  Env Con-F1

dit-htN---------r--V----Ri-q-------a-k-Q-t---------i--skdidek--L--i------------------r-------------q----a----  Env Con-F2

......N-------k----Vr---r--q-------a-n-t-r------i--------ts-n-t------------------------k-------r-R----e------  Env Con-G

sk------...............ent---i------------r--q-I-----a-n-t-t------i------nrsetg--t----------------------q----  Env Con-J

......dt----------------k----I-----a-s-n-r-----mi------.-dthe-t----------------------q-----i---r-r-----------  Env Con-K

......nt---i------------r--q-I-----a-n-t-t------i------rsetg--t----------------------q-----i---r-r-----------  Env Con-J

......n-----------------r----------a-n-t------------------s-n-t----------------------------------------------  Env Con-Con

tegsnntdtitlpCrIk (17) [-0.75] 

       dtitlpCrIkqiiNmw (16) [0.21] 

             CrIkqiiNmwQeVgkamY (18) [-0.17] 

                     mwQeVgkamYApPirGqi (18) [-0.25] 

                             mYApPirGqirCsSnI (16) [-0.17] 

                                   rGqirCsSnITGllLtr (17) [-0.08] 

                                          SnITGllLtrdggnnnnt (18) [-0.76] All C-term AAs forbidden

                                                  trdggnnnntteiFr (15) [-1.71] 

                                                       nnnntteiFrpgggdmr (17) [-1.47] 

                                                              iFrpgggdmrdnwrseLy (18) [-1.13] 

                                                                      mrdnwrseLykYKvvki (17) [-0.99] 

                                                                             eLykYKvvkieplgvA (16) [0.20] 

                                                                                   vvkieplgvAPTkakRRv (18) [0.01] 

                                                                                           vAPTkakRRvvqrEkrav (18) [-0.93] 

RvvqrEkravgigamflGFLgaAGSTMGAasmtLTvQaRqllsGIvqQQnnLLrAieaQQhllqLTvwGiKQLQarvLaverYLkdQqLlgiwGCsgklictTavpwnasw  Env Con-B

--------------L-------------------------------------------------------------I----------------------------------  Env HXB2

--------------V----------------I-----------------------------M----------------------Q------------------T----T--  Env DH123

---e-------l--v-i--------------I-----------------s-------------k---------------------------------------n----s--  Env Con-A

---e----------v----------------I-----------------s-----------m------------t----i----------------------------s--  Env Con-C

---e-----i-l-------------------v------------------------------------------------------------------h----n----s--  Env Con-D

q-----r-------l----------------i-----------------------------------------------------------------------N----s--  Env Con-F1

q----a-----M---l--------------aI---a-------------S---K----------------------I------------------------p-t----s--  Env Con-F2

---e-------l--v----------------i-----v-----------s-----------------------------------------------------n----t--  Env Con-G

-----q-----i---r-r---------------v----------------I-----------------s------------------------------------------  Env Con-J

-----------l--l----------------I-----------------------------------------r----------r------------------n----s--  Env Con-K

--------------v----------------I-----------------s-----------------------------------------------------n----s--  Env Con-J

--------------v----------------i-----------------s-----------------------------------------------------n----s--  Env Con-Con

RvvqrEkravgigamfl (17) [0.24] 

       ravgigamflGFLgaA (16) [1.56] 

             amflGFLgaAGSTMGAa (17) [1.35] 

                    gaAGSTMGAasmtLTvQa (18) [0.69] 

                            AasmtLTvQaRqllsGIv (18) [0.93] 

                                   vQaRqllsGIvqQQnnLL (18) [-0.02] 

                                           GIvqQQnnLLrAieaQQh (18) [-0.65] 

                                                   LLrAieaQQhllqLTvw (17) [0.47] 

                                                         aQQhllqLTvwGiKQLQa (18) [0.05] 

                                                                 TvwGiKQLQarvLaverY (18) [0.09] 

                                                                        LQarvLaverYLkdQqLl (18) [-0.04] 

                                                                                erYLkdQqLlgiwGCsgk (18) [-0.67] 

                                                                                        LlgiwGCsgklictTav (17) [1.36] 

                                                                                               sgklictTavpwnasw (16) [0.28] 

tTavpwnaswsnksldqiwnnmTwmewereidnytsliytLieesqnqQekNeqeLleLdkwaslwnwfdItnWLwYikiFimivgGLvGLrivfavlsivnrvRqgy  Env Con-B

---------------E----HT-----D---N------HS-----------------------------N---------L----------------------------  Env HXB2

--T----T--------T--G-----Q--K--N---G---N-----------------A-----------N-S----------------I------S------------  Env DH123

--n----s------qse--d----Lq-dk--s---qi--q--------------d--a-----n-------s----------------I-----------i-------  Env Con-A

-------s------qee--d-----q-d---s---nt--r-L-d---------kd--a--s-qn------------------------I----i--------------  Env Con-C

--n----s-------ee--q---------------g---s------i----------------------s--q---------------I-------------------  Env Con-D

--N----s------q-E--------q--K--s--Skt--r-----------------a--------s----s----------------I----------------K--  Env Con-F1

p-t----s------y-d--d-----q--K------kT--r---sA-----r---d--A----D---s--S--r-----------i-s-I-----------i-------  Env Con-F2

--n----t------yne--d----i--d---s---qq--s--------------D--A------------------------------I-------------------  Env Con-G

---------------------n----s------yee--e-----q--k--n---gt--s----a---------d--a-------------s------------i---i  Env Con-J

--n----s------qse--------q--k--r--s-t--r------i-------d--a--------------k---------------i----a-----v--------  Env Con-K

--n----s------yee--e-----q--k--n---gt--s----a---------d--a-------------s------------i---i----i--------------  Env Con-J

--n----s------q-e--d-----q--k--s---qt--s--------------d--a------------------------------i-------------------  Env Con-Con

tTavpwnaswsnksldqi (18) [-0.50] 

        swsnksldqiwnnmTwm (17) [-0.89] 

               dqiwnnmTwmewerei (16) [-1.23] 

                     mTwmewereidnytsliy (18) [-0.67] 

                             eidnytsliytLieesqn (18) [-0.50] All C-term AAs forbidden

                                     iytLieesqnqQekNeqeL (19) [-1.51] 

                                              nqQekNeqeLleLdkwa (17) [-1.79] 

                                                    eqeLleLdkwaslwnwf (17) [-0.51] 

                                                           dkwaslwnwfdItnWLwY (18) [-0.47] 

                                                                   wfdItnWLwYikiFimiv (18) [1.24] 

                                                                           wYikiFimivgGLvGLri (18) [1.74] 

                                                                                   ivgGLvGLrivfavlsiv (18) [2.44] 

                                                                                           rivfavlsivnrvRqgy (17) [0.66] 

sivnrvRqgysplSfqtrlPaprgpdrPegieeeggerdrdrsgrlvdgflaliwvdlrslclfsyhrlrdLllivtrivelLgrrGweaLkYwwnllqYwsqelknSavsll  Env Con-B

-----------------H--T----------------------I---N-S-----D---------------------------------------------------------  Env HXB2

------------------F--S--------------D------SP-------I------T-F---------------------------L---L-------------------  Env DH123

--i--------------ht-n---l---gr-------Q-----I---s-----a-d---------------fi--aa-t------l---G---L----l--gr---i--in--  Env Con-A

-----------------lt-n------lgr-------Q-----i---s-----a-d----------------i--aa-a-----q--------LGs-v---gl---k--i---  Env Con-C

-----------------l-------------------qg----i---n--s----D---n------------I--Aa-------.--------L---------------i---  Env Con-D

-------K------l--lI-s--e---------G---Qgk---V---t-----a-D---N------RH---FI--AA---....---------Lg--t-----------I---  Env Con-F1

--i-----------L--LI-N-------G--------p-----i---S---p-a-D------s----h----i--AA-T-....k--------L---a-h-G-------I---  Env Con-F2

-----------------Lthhq-e---------g---Q-----i---s---p-a-d---------------fi--aa-T------l---g---L----l--g-------In--  Env Con-G

-----i---i----i---------------------Li-t---a--------g---Q--t--v---s-----a-d---n------------v--a---l-t-......gl.--  Env Con-J

-v---------------Li-t------------g---Q-k---V---S-----a-d---N------rh----i--a---L-r-.q--------L---i---g-------I---  Env Con-K

-----------------Li-t---a--------g---Q--t--v---s-----a-d---n------------v--a---l-t-..--------L---vw--g-------I---  Env Con-J

-----------------li-n----------------q-----i---s-----a-d----------------i--aa----------------l-------g-------i---  Env Con-Con

sivnrvRqgysplSfqtr (18) [-0.61] 

        gysplSfqtrlPapr (15) [-0.61] 

             SfqtrlPaprgpdrPegi (18) [-1.10] 

                     prgpdrPegieeegger (17) [-2.14] 

                            egieeeggerdrdrsgrl (18) [-2.03] 

                                    erdrdrsgrlvdgflali (18) [-0.49] 

                                            rlvdgflaliwvdlrsl (17) [1.08] 

                                                   aliwvdlrslclfsyhrl (18) [0.85] 

                                                           slclfsyhrlrdLlliv (17) [1.07] 

                                                                  hrlrdLllivtrivelL (17) [0.93] 

                                                                         livtrivelLgrrGweaL (18) [0.64] 

                                                                                 lLgrrGweaLkYwwnll (17) [-0.23] 

                                                                                        eaLkYwwnllqYwsqelk (18) [-0.80] 

                                                                                                llqYwsqelknSavsll (17) [0.15] 

elknSavsllnatAiavaegtDrvievvqracrailhiprrirqGlerall  Env Con-B

-----------------------------G-----R------------I--  Env HXB2

-----------------G-----I--IL---G----N--T-----------  Env DH123

---i--in--Dti-----gW------ig--ig----n--------f-----  Env Con-A

---k--i---dti----------i--li--i----rn--------f-a--q  Env Con-C

------i---dt--------------i-------v-n--------------  Env Con-D

------I----t---v----------aL---g--v-N--------------  Env Con-F1

------I---Dri----------I--iL---G--V----------a-----  Env Con-F2

------In--dTi-----nw-------a--------n--------------  Env Con-G

.....gl.--....------L---vw--g-------I----T---------  Env Con-J

------I----T-----------I--ia---f--l----------------  Env Con-K

------I----T-----------I--ia---f-------------------  Env Con-J

------i---dt--------------ia--------n--------------  Env Con-Con

elknSavsllnatAiava (18) [0.92] 

        llnatAiavaegtDrvi (17) [0.91] 

               avaegtDrvievvqracr (18) [0.03] 

                       vievvqracrailhiprr (18) [0.34] 

                               crailhiprrirqGlera (18) [-0.42] 

                                       rrirqGlerall (12) [-0.64] 



Nef[Number of peptides generated: 27]

mggkwSkrsvvgWptvrermrraepaadgvgAvsrdlekhgaitssntaannadcawleaqeeeevgfpvrpqvplrPmtykaavDlshFlkekGglegliysqk  Nef Con-B

-------S--I-----------------R---A-----------------T--A----------------T------------------------------H--R  Nef HXB2

----L--CGG---S--------------R---A----G------------T----------Q-----------I----------L--------------------  Nef DH123

-------s-i----q----i-qtp---e------Q--d----v----..i-----v--------------------------g-f---f--------d-----k-  Nef Con-A

-------c-i----ai------t----e----a-q--d-y--l-----dtt-------r---------------------f-g-f---f--------------k-  Nef Con-C

-------S-i----Ai---i--Td-------------------------sT--a---------s------------------e------------------w-k-  Nef Con-D

-------S-I----AI------pP---E------Q---RR--------r-t-P-L-------dd------------------G-------xx--------x--Kr  Nef Con-F

-------s-i----a----i-qtP---E------Q--ar----------t--p----------dS-------------------f---F--------D-----K-  Nef Con-G

-------sris---a----i-------e---------DRR--V-IN---st-p-a--------a------------------g-f------------d-----K-  Nef Con-H

--n----S....--q--------p--PaA-----Q--A------------t----------t-----------x--------g-f---F--------d-----k-  Nef Con-J

--na---skfa---e--r-----rsppcA--q---e-aar-g-p--h-Pq---aL-f--shqd---------------------F---f--------------h-  Nef Con-O

-------s-i----a--------p----------q---------------t-------------------------------g-f---f--------------k-  Nef Con-Con

mggkwSkrsvvgWptvr (17) [-0.54] 

       rsvvgWptvrermrra (16) [-0.88] 

             ptvrermrraepaadgv (17) [-1.01] 

                    rraepaadgvgAvsrdl (17) [-0.46] 

                           dgvgAvsrdlekhgai (16) [-0.24] 

                                 srdlekhgaitssntaa (17) [-0.74] 

                                        gaitssntaannadcawl (18) [0.08] 

                                                aannadcawleaqeeeev (18) [-0.72] 

                                                        wleaqeeeevgfpvrpqv (18) [-0.69] 

                                                                evgfpvrpqvplrPmtyk (18) [-0.42] 

                                                                       pqvplrPmtykaavDlsh (18) [-0.26] 

                                                                               tykaavDlshFlkekGgl (18) [-0.19] 

                                                                                       shFlkekGglegliysqk (18) [-0.60] 

glegliysqkrqdILdlwvyhTQGyfpDwqnyTpgpgiryPltfgWcfkLVPvepekveeanegennsllhPmslHgmddperevlewkfDsrlafhhmarelhPeyykdc  Nef Con-B

------H--R--------I---------0-------V---------Y-------D-I----K---T-----V---------------R---------V--------F-N-  Nef HXB2

--------------------N--------------------------------D-----A-------C----I-----E---K---L--------Y-------------N-  Nef DH123

--d-----k---e-------n---f-----------------c----------d-re---d-k----c------Q--ie-e-----m-----a--rk-i-------f----  Nef Con-A

--------k---e------------------------v---------------D-re--------d-c----vcq---e-eh----q-----q--hr-r-------f----  Nef Con-C

------w-k---e-----------i-----------------------e----d-qe----T---d-c----icQ---E----q--v-R-N-----E-K---k--------  Nef Con-D

-----x--Kr--E-----l------------------------m---------d--E--K-------C------Q---E-ED----K--------Lr-I---R-----q-  Nef Con-F

--D-----K-----------n---f------------t-f------------md-aE-----k---------iCQ---E-eD----v-R---S--Rr-l------------  Nef Con-G

--d-----K---e-------N----------------E---------------d-Qe--q-------------cq---E-------M--------lt-r---k---f----  Nef Con-H

--d-----k---e------hn--------------------------------d-sE----------c----iCQ--ie-e-----q-----S--RR-i-------F----  Nef Con-J

--------h--aE-----------F------------t-F------l------se-ea-q--ttcdaa----pcq--ae-ahk-i-k-q--rs-glt-i--iq---ss-s-  Nef Con-O

--------k---e----------------------------------------d--e----------c-----cq---e-e-----m--------rr-i------------  Nef Con-Con

glegliysqkrqdILdlw (18) [-0.31] 

       sqkrqdILdlwvyhTQGy (18) [-1.01] 

               dlwvyhTQGyfpDwqny (17) [-1.08] 

                     TQGyfpDwqnyTpgpgir (18) [-1.23] 

                            wqnyTpgpgiryPltfgW (18) [-0.68] 

                                    giryPltfgWcfkLVPv (17) [0.78] 

                                           fgWcfkLVPvepekveea (18) [0.00] 

                                                   Pvepekveeanegennsl (18) [-1.43] 

                                                           eanegennsllhPmslH (17) [-0.94] 

                                                                  nsllhPmslHgmddper (17) [-0.88] 

                                                                         slHgmddperevlewkf (17) [-0.96] 

                                                                                perevlewkfDsrlafhh (18) [-0.97] 

                                                                                        kfDsrlafhhmarelh (16) [-0.72] 

                                                                                              afhhmarelhPeyykdc (17) [-1.06] 



last modified: Wed Nov 4 13:57 2009


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