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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


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