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LOCUS JX446738 5063 bp RNA linear VRL 12-OCT-2012
DEFINITION HIV-1 isolate AA006a08L from Thailand gag protein (gag) gene,
complete cds; pol protein (pol) gene, partial cds; and vif protein
(vif) and vpr protein (vpr) genes, complete cds
ACCESSION JX446738
VERSION JX446738.1 GI:407732291
KEYWORDS .
SOURCE Human immunodeficiency virus 1 (HIV-1)
ORGANISM Human immunodeficiency virus 1 Viruses; Retro-transcribing viruses;
Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus
group
REFERENCE 1 (bases 1 to 5063)
Show all sequences for reference 1
AUTHORS Rolland,M., Edlefsen,P.T., Larsen,B.B., Tovanabutra,S.,
Sanders-Buell,E., Hertz,T., deCamp,A.C., Carrico,C., Menis,S.,
Magaret,C.A., Ahmed,H., Juraska,M., Chen,L., Konopa,P., Nariya,S.,
Stoddard,J.N., Wong,K., Zhao,H., Deng,W., Maust,B.S., Bose,M.,
Howell,S., Bates,A., Lazzaro,M., O'Sullivan,A., Lei,E.,
Bradfield,A., Ibitamuno,G., Assawadarachai,V., O'Connell,R.J.,
deSouza,M.S., Nitayaphan,S., RERKS-NGARM,S., Robb,M.L.,
McLellan,J.S., Georgiev,I., Kwong,P.D., Carlson,J.M., Michael,N.L.,
Schief,W.R., Gilbert,P.B., Mullins,J.I. and Kim,J.H.
TITLE Increased HIV-1 vaccine efficacy against viruses with genetic
signatures in Env V2.
JOURNAL Nature.. 490(7420); 417-20 (2012)
PUBMED 22960785
REFERENCE 2 (bases 1 to 5063)
Show all sequences for reference 2
AUTHORS Rolland,M., Edlefsen,P.T., Larsen,B.B., Tovanabutra,S.,
Sanders-Buell,E., Hertz,T., de Camp,A.C., Carrico,C., Menis,S.,
Magaret,C.A., Ahmed,H., Juraska,M., Chen,L., Konopa,P., Nariya,S.,
Stoddard,J.N., Wong,K., Zhao,H., Deng,W., Maust,B.S., Bose,M.,
Howell,S., Bates,A., Lazzaro,M., O'Sullivan,A., Lei,E.,
Bradfield,A., Ibitamuno,G., Assawadarachai,V., O'Connell,R.J., de
Souza,M.S., Nitayaphan,S., RERKS-NGARM,S., Robb,M.L.,
McLellan,J.S., Georgiev,I., Kwong,P.D., Carlson,J.M., Michael,N.L.,
Schief,W.R., Gilbert,P.B., Mullins,J.I. and Kim,J.H.
TITLE Direct Submission
JOURNAL Submitted (01-AUG-2012) US Military HIV Research Program, 503
Robert Grant Ave, Silver Spring, MD 20910, USA
COMMENT ##Assembly-Data-START## Sequencing Technology Sanger dideoxy
sequencing ##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..5063
/organism="Human immunodeficiency virus 1"
/mol_type="genomic RNA"
/isolate="AA006a08L"
/isolation_source="plasma AA006a"
/host="Homo sapiens; RV144 trial participant AA006"
/db_xref="taxon:11676"
/country="Thailand"
/collection_date="2006"
/note="subtype: CRF01_AE"
gene 2..1504
/gene="gag"
CDS 2..1504
/gene="gag"
/codon_start="1"
/transl_table="1"
/product="gag protein"
/protein_id="AFU26218.1"
/db_xref="GI:407732292"
/translation="MGARASVLSGGKLDAWEKIRLRPGGKKKYRMKHLVWASRELERF
ALNPELLETAEGCQQLIEQLQSTLKTGSEELRSLFNLIATLWCVHQRIEIKDTKEALE
KIEKIQNKSQQQTQQAAAGTGSSSKVSQNYPIVQNAQGQMVHSPLSPRTLNAWVKVVE
EKGFNPEVIPMFSALSEGATPQDLNMMLNIVGGHQAAMQMLKETINEEAAEWDRIHPV
HAGPIPPGQMREPRGSDIAGTTSTLQEQIGWMTSNPPIPVGEIYKRWIILGLNKIVRM
YSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNANPDCKSIL
KALGTGATLEEMMTACQGVGGPSHKARVLAEAMSHVQHANIMMQRGNFRNQGQKRIKC
FNCGKEGHLARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFPQ
SRPEPTAPPAEDWGTGEETTSLLKQEQKDKGHPPPLVSLKSLFGNDPLSQ"
misc_feature 5..>331
/gene="gag"
/note="gag gene protein p17 (matrix protein); Region:
Gag_p17; pfam00540"
/db_xref="CDD:109591"
misc_feature 446..1090
/gene="gag"
/note="gag gene protein p24 (core nucleocapsid protein);
Region: Gag_p24; pfam00607"
/db_xref="CDD:201337"
misc_feature 1169..1222
/gene="gag"
/note="Zinc knuckle; Region: zf-CCHC; pfam00098"
/db_xref="CDD:189387"
misc_feature 1232..1285
/gene="gag"
/note="Zinc knuckle; Region: zf-CCHC; pfam00098"
/db_xref="CDD:189387"
misc_feature 1346..1453
/gene="gag"
/note="Gag protein p6; Region: Gag_p6; pfam08705"
/db_xref="CDD:149684"
gene <1297..4308
/gene="pol"
CDS <1297..4308
/gene="pol"
/codon_start="1"
/transl_table="1"
/product="pol protein"
/protein_id="AFU26219.1"
/db_xref="GI:407732293"
/translation="FFRENLAFQQGEARQFSPEQTRANSPTSRRLGDGGRDNLLAEAG
AERQGTPSSLSFPQITLWQRPLVTVKIGGQLKEALLDTGADDTVFEEISLSGKWKPKM
IGGIGGFIKVRQYDQILIEICGKKAIGTVLVGPTPVNIIGRNMLTQVGCTLNFPISPI
DTVPVALKPGMDGPKVKQWPLTEEKIKALTEICKEMEEEGKISKIGPENPYNTPVFAI
KKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLD
ESFRKYTAFTIPSTNNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRIKNPEIV
IYQYMDDLYVGSDLEIGQHRIKIEELRAHLLSWGFTTPDKKHQKEPPFLWMGYELHPD
RWTVQPVKLPEKDSWTVNDIQKLVGKLNWASQIYAGIKVKQLCKLLRGAKALTDIVPL
TEEAELELAENREILKTPVHGVYYDPSKDLVAEVQKQGQDQWTYQIYQEPFKNLKTGK
YARKRSAHTNDVRQLTEVVQKIVTESIVIWGKAPKFRLPIQKETWDTWWMEYWQATWI
PEWEFVNTPPLVKLWYQLEKDPIVGAETFYVDGAASRETKLGKAGYVTDRGRQKVVTL
TETTNQKTELHAIHLALQDSGSEVNIVTDSQYALGIIQAQPDRSESEVVNQIIEDLIK
KERVYLSWVPAHKGIGGNEQVDKLVSTGIRKVLFLDGIDKAQEDHERYHSNWRTMASD
FNLPPIIAKEIVANCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGY
IEAEVIPAETGQETAYFLLKLAGRWPVKVIHTDNGSNFTSNAVKAACWWANVRQEFGI
PYNPQSQGVVESMNKELKKIIGQVREQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGER
IIDIIATDIQTKELQKQITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDI
KVVPRRKAKIIRDYGKQMAGDDCVAGRQDED"
misc_feature 1495..1737
/gene="pol"
/note="Retropepsins, pepsin-like aspartate proteases;
Region: HIV_retropepsin_like; cd05482"
/db_xref="CDD:133149"
misc_feature order(1537..1539,1543..1545,1549..1551,1600..1608,1714..17
16)
/gene="pol"
/note="inhibitor binding site; inhibition site"
/db_xref="CDD:133149"
misc_feature 1537..1545
/gene="pol"
/note="catalytic motif [active]"
/db_xref="CDD:133149"
misc_feature 1537..1539
/gene="pol"
/note="Catalytic residue [active]"
/db_xref="CDD:133149"
misc_feature order(1600..1614,1618..1632)
/gene="pol"
/note="Active site flap [active]"
/db_xref="CDD:133149"
misc_feature 1813..2463
/gene="pol"
/note="RT_Rtv: Reverse transcriptases (RTs) from
retroviruses (Rtvs). RTs catalyze the conversion of
single-stranded RNA into double-stranded viral DNA for
integration into host chromosomes. Proteins in this
subfamily contain long terminal repeats (LTRs) and...;
Region: RT_Rtv; cd01645"
/db_xref="CDD:73152"
misc_feature order(1831..1836,1942..1944,1954..1956,1975..1977,1981..19
89,1993..1995,2002..2004,2026..2028,2032..2037,2041..2043,
2089..2106,2212..2217,2221..2223,2230..2232,2308..2310,231
4..2319,2449..2454)
/gene="pol"
/note="active site"
/db_xref="CDD:73152"
misc_feature order(1831..1836,1981..1989,1993..1995,2002..2004,2026..20
28,2032..2037,2041..2043,2215..2217,2221..2223,2230..2232,
2308..2310,2449..2454)
/gene="pol"
/note="DNA binding site [nucleotide binding]"
/db_xref="CDD:73152"
misc_feature 1948..2463
/gene="pol"
/note="Reverse transcriptase (RNA-dependent DNA
polymerase); Region: RVT_1; pfam00078"
/db_xref="CDD:200982"
misc_feature order(1954..1956,1975..1977,2089..2106,2212..2214,2314..23
16)
/gene="pol"
/note="dNTP binding site [chemical binding]; other site"
/db_xref="CDD:73152"
misc_feature order(2059..2070,2296..2298,2302..2304,2323..2325,2329..23
31,2440..2442)
/gene="pol"
/note="NNRTI binding site; other site"
/db_xref="CDD:73152"
misc_feature 2473..2682
/gene="pol"
/note="Reverse transcriptase thumb domain; Region:
RVT_thumb; pfam06817"
/db_xref="CDD:115473"
misc_feature 2710..3018
/gene="pol"
/note="Reverse transcriptase connection domain; Region:
RVT_connect; pfam06815"
/db_xref="CDD:203523"
misc_feature 3067..3432
/gene="pol"
/note="RNase H; Region: RNase_H; pfam00075"
/db_xref="CDD:200979"
misc_feature order(3088..3096,3100..3102,3181..3186,3193..3195,3253..32
55,3364..3366)
/gene="pol"
/note="RNA/DNA hybrid binding site [nucleotide binding];
other site"
/db_xref="CDD:187690"
misc_feature order(3088..3090,3253..3255)
/gene="pol"
/note="active site"
/db_xref="CDD:187690"
misc_feature 3463..3582
/gene="pol"
/note="Integrase Zinc binding domain; Region:
Integrase_Zn; pfam02022"
/db_xref="CDD:202092"
misc_feature 3613..3927
/gene="pol"
/note="Integrase core domain; Region: rve; pfam00665"
/db_xref="CDD:201381"
misc_feature 4099..4251
/gene="pol"
/note="Integrase DNA binding domain; Region: IN_DBD_C;
pfam00552"
/db_xref="CDD:144223"
gene 4253..4831
/gene="vif"
CDS 4253..4831
/gene="vif"
/codon_start="1"
/transl_table="1"
/product="vif protein"
/protein_id="AFU26220.1"
/db_xref="GI:407732294"
/translation="MENRWQVMIVWQVDRMRIRTWNSLVKHHMYISRKAKKWFYKHHY
ESQHPKVSSEVHIPLGEAILVIKTYWGLQTGEKDWQLGHGVSIEWRQRTYRTQIDPDL
ADQLIHLQYFECFSESAIRKAILGQVVRRRCEYPSGHNKVGSLQYLALKALTTPKRVR
PPLPSVKKLTEDRWNKPQKIRDHRENPTMNGH"
misc_feature 4253..4828
/gene="vif"
/note="Retroviral Vif (Viral infectivity) protein; Region:
Vif; pfam00559"
/db_xref="CDD:109609"
gene 4771..5061
/gene="vpr"
CDS 4771..5061
/gene="vpr"
/codon_start="1"
/transl_table="1"
/product="vpr protein"
/protein_id="AFU26221.1"
/db_xref="GI:407732295"
/translation="MEQAPEDQGPQREPYNEWTLELLEELKNEAVRHFPRPWLHGLGQ
YIYNTYGDTWEGVEAIIRILQQLLFVHFRIGCQHSRIGIIPGRRGRNGANRS"
misc_feature 4771..5007
/gene="vpr"
/note="VPR/VPX protein; Region: VPR; pfam00522"
/db_xref="CDD:109573"
BASE COUNT 1942 a 862 c 1189 g 1070 t
ORIGIN
1 gatgggtgcg agagcgtcag tattaagtgg gggaaaatta gatgcatggg aaaaaattcg
61 gttacggcca gggggaaaga aaaaatatag gatgaaacat ttagtatggg caagcagaga
121 gttagaaaga ttcgcactta accctgagct tctagaaaca gcagaaggat gtcaacaact
181 catagaacag ttacagtcaa ctctcaagac aggatcagag gaacttagat cattatttaa
241 tttaatagca accctctggt gcgtacacca gaggatagag ataaaagaca ccaaggaagc
301 tctagagaag atagagaaaa tacaaaataa gagccagcaa cagacacagc aggcagcagc
361 tggcacagga agcagcagca aagtcagcca aaattaccct atagtgcaaa atgcacaagg
421 gcaaatggta cacagtcctt tatcacccag gactttgaac gcatgggtga aagtagtaga
481 agaaaagggt tttaacccag aagtaatacc catgttctca gcattatcag agggagccac
541 cccacaagat ctaaatatga tgctaaatat agtgggggga caccaggcag caatgcaaat
601 gttaaaagaa accatcaatg aggaagctgc agaatgggat aggatacacc cagtacatgc
661 agggcctatt ccaccaggcc agatgaggga accaagggga agtgacatag caggaactac
721 tagcaccctt caagaacaaa taggatggat gacaagcaat ccacctatcc cagtgggaga
781 aatctataaa aggtggataa tcctgggctt aaataaaata gtaagaatgt atagccctgt
841 tagcattttg gacataagac aagggccaaa agaacccttt agagactatg tagataggtt
901 ctataaaact ctccgagcgg aacaagctac acaggaggta aaaaactgga tgacagaaac
961 cttgctagtc caaaatgcga atccagactg taagtccatt ttaaaagcat taggaacagg
1021 agctacatta gaagaaatga tgacagcatg ccagggagtg ggaggaccta gccataaagc
1081 aagggttttg gctgaagcaa tgagccacgt gcaacatgca aatataatga tgcagagagg
1141 caattttagg aaccagggtc aaaaaagaat taagtgcttc aactgtggca aagaaggaca
1201 cctagccaga aattgcaggg cccctaggaa aaagggttgt tggaaatgtg ggaaagaagg
1261 acatcaaatg aaagactgca ctgaaagaca ggctaatttt ttagggaaaa tttggccttc
1321 caacaagggg aggccaggca attttcccca gagcagacca gagccaacag ccccaccagc
1381 agaagactgg gggacggggg aagagacaac ctccttgctg aagcaggagc agaaagacaa
1441 gggacaccct cctcccttag tttccctcaa atcactcttt ggcaacgacc ccttgtcaca
1501 gtaaaaatag gagggcagct gaaggaagct ctattagata caggagcaga tgatacagta
1561 tttgaagaga taagtttgtc aggaaaatgg aaaccaaaaa tgataggggg aattggaggt
1621 tttatcaagg taaggcaata tgatcagata cttatagaaa tttgtggaaa aaaggctata
1681 ggtacagtat tagtaggacc tacacctgtc aacataattg gaaggaatat gttgactcag
1741 gttggttgta ctttaaattt cccaattagt cctattgaca ctgtaccagt agcattaaag
1801 ccaggaatgg atggaccaaa ggttaaacaa tggccattga cagaagaaaa aataaaagcg
1861 ttaacagaaa tctgtaaaga gatggaagag gaaggaaaaa tctcaaaaat tgggcctgaa
1921 aatccataca atactccagt atttgctata aagaaaaagg acagcaccaa atggaggaaa
1981 ttagtagatt tcagagagct caacaaaaga actcaggact tttgggaagt tcaattagga
2041 ataccacatc cagcaggttt aaaaaagaaa aaatcagtaa cagtactaga tgtgggagat
2101 gcatattttt cagttccttt agatgaaagt tttagaaagt atactgcatt taccatacct
2161 agtacaaaca atgagacacc aggaatcaga tatcagtaca atgtgctgcc acagggatgg
2221 aaagggtcac cggcaatatt ccagagtagc atgacaaaaa tcttagagcc ctttagaata
2281 aaaaatccag aaatagttat ctatcaatac atggatgact tgtatgtagg atctgattta
2341 gaaatagggc agcacagaat aaaaatagag gagctgagag ctcatctatt gagctggggg
2401 tttactacac cagacaaaaa gcatcagaag gaacctccat tcctttggat gggatatgaa
2461 ctccatcctg acagatggac agtccagcct gtaaaactgc cagaaaaaga cagctggact
2521 gtcaatgata tacagaaatt agtgggaaaa ctaaattggg caagtcaaat ttatgcagga
2581 attaaggtaa agcaactgtg taaacttctc aggggagcta aagcactaac agacatagta
2641 ccactgactg aagaagcaga attagagttg gcagagaaca gggagatttt aaaaacccct
2701 gtgcatggag tatattatga cccatcaaaa gacttagtag cagaagtaca gaaacaaggg
2761 caagaccaat ggacatatca aatttatcaa gagccattta aaaatctaaa aacaggaaaa
2821 tatgccagaa aaagatctgc tcacactaat gatgtaagac aattaacaga agtggtgcaa
2881 aaaatagtca cagaaagcat agtaatatgg ggaaaggccc ctaaatttag gctacccata
2941 caaaaagaaa catgggatac atggtggatg gagtattggc aggctacatg gattcctgaa
3001 tgggagtttg ttaatacccc tcctctagta aaattatggt accaattaga aaaagacccc
3061 atagtaggag cagagacttt ctatgtagat ggggcagcta gtagggagac caagctagga
3121 aaggcagggt atgtcactga cagaggaaga caaaaggtag ttaccctaac tgagacaaca
3181 aatcaaaaga ctgaattaca tgcaatacac ttagccttac aggattcagg atcagaagta
3241 aatatagtaa cagactcaca atatgcatta ggaatcattc aggcacaacc agataggagt
3301 gaatcagaag tagtcaacca aataatagag gatctaataa aaaaggaaag ggtctacctg
3361 tcatgggtac cagcacacaa gggaattgga ggaaatgaac aagtagataa attagtcagt
3421 acaggaatca gaaaagtgct atttttagat gggatagata aggcccaaga agaccatgaa
3481 agatatcaca gcaattggag aacaatggct agtgatttta atttgccacc tataatagca
3541 aaggaaatag tagccaactg tgataaatgt caactaaaag gggaagctat gcatggacaa
3601 gtagactgta gtccagggat atggcaatta gattgcacac atctagaagg aaaagtcatt
3661 ctggtagcag tccacgtggc cagtggatat atagaagcag aagttatccc agcagaaaca
3721 ggacaagaga cagcatactt tttattaaaa ttagcaggaa gatggccagt aaaagtaata
3781 cacacagaca atggtagcaa tttcaccagc aatgcagtta aagcagcctg ttggtgggcc
3841 aatgtccggc aggaatttgg gatcccttac aatccccaaa gtcaaggagt agtagaatct
3901 atgaataagg aattaaagaa aatcataggg caggtaagag agcaagctga acaccttaag
3961 acagcagtac aaatggcagt attcattcac aattttaaaa gaaaaggggg gattgggggg
4021 tacagtgcag gagaaagaat aatagacata atagcaacag acatacaaac taaagaatta
4081 caaaaacaaa ttacaaaaat tcaaaatttt cgggtttatt acagggacag cagagaccca
4141 atttggaaag gaccagcaaa actactctgg aaaggtgaag gggcagtagt aatacaagac
4201 aatagtgata taaaagtagt accaagaaga aaagcaaaga tcattaggga ttatggaaaa
4261 cagatggcag gtgatgattg tgtggcaggt agacaggatg aggattagaa catggaacag
4321 tttagtaaaa catcatatgt atatctcaag gaaagctaaa aagtggtttt ataaacatca
4381 ttatgaaagc cagcatccaa aggtaagttc agaagtacat atcccactag gagaggctat
4441 attagtaata aaaacatatt ggggtctgca gacaggagaa aaggattggc aattgggtca
4501 tggagtctcc atagaatgga ggcagagaac atataggaca caaatagatc ctgacctagc
4561 agaccaactg attcatctac aatattttga atgtttttca gaatctgcca taaggaaagc
4621 catattagga caagtagtta gacgtaggtg tgaatatccg tcaggacata acaaggtagg
4681 atccttacaa tatttggcgc tgaaagcatt aacaacacca aaaagggtaa ggccacctct
4741 gcctagtgtt aaaaaattaa cagaagatag atggaacaag ccccagaaga tcagggacca
4801 cagagagaac cctacaatga atggacatta gaactgttag aggagcttaa aaatgaagct
4861 gttagacatt ttcctaggcc ctggctccat ggcttaggac agtacatcta taacacttat
4921 ggagatactt gggaaggggt agaagctata ataagaattt tgcaacaact actgtttgtt
4981 catttcagaa ttgggtgtca acatagcaga ataggcatta taccagggag aagaggcagg
5041 aatggagcca atagatccta acc
//
last modified: Tue May 31 10:56 2022