BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy14859
(1097 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B3O|B Chain B, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique
Rt Conformation And Substrate Interface
Length = 441
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 63/279 (22%), Positives = 118/279 (42%), Gaps = 38/279 (13%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRI-- 538
EM + G + ++ + + +F + K +G R +++ + LN KK ++
Sbjct: 41 EMEKEGKISKIGPENPYNTPVFAIKKKDGTKWRKLVDFRELN-----KKTQDFWEVQLGI 95
Query: 539 --PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLA 589
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G
Sbjct: 96 PHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWK 155
Query: 590 TAPQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWI 647
+P F S + R + +V+ Y+DD L V D I + + K+ L W
Sbjct: 156 GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWG 214
Query: 648 VNLQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLL 707
+ P FL + ++ H D+ T+ I+ L +W ++ + L+
Sbjct: 215 LTTPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLV 262
Query: 708 GYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
G L++AS + P ++++ LLR G LT + P
Sbjct: 263 GKLNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 295
>pdb|4B3P|B Chain B, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique
Rt Conformation And Substrate Interface
pdb|4B3Q|B Chain B, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique
Rt Conformation And Substrate Interface
Length = 454
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 63/279 (22%), Positives = 118/279 (42%), Gaps = 38/279 (13%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRI-- 538
EM + G + ++ + + +F + K +G R +++ + LN KK ++
Sbjct: 54 EMEKEGKISKIGPENPYNTPVFAIKKKDGTKWRKLVDFRELN-----KKTQDFWEVQLGI 108
Query: 539 --PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLA 589
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G
Sbjct: 109 PHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWK 168
Query: 590 TAPQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWI 647
+P F S + R + +V+ Y+DD L V D I + + K+ L W
Sbjct: 169 GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWG 227
Query: 648 VNLQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLL 707
+ P FL + ++ H D+ T+ I+ L +W ++ + L+
Sbjct: 228 LTTPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLV 275
Query: 708 GYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
G L++AS + P ++++ LLR G LT + P
Sbjct: 276 GKLNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 308
>pdb|4HKQ|A Chain A, Protein Dna Complex
Length = 681
Score = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 63/276 (22%), Positives = 118/276 (42%), Gaps = 29/276 (10%)
Query: 426 LRRFVDAWIRLGA------PAPLVRIVSGYAIPFSAKPPLVPLCSLQHLATPVSSAMSLH 479
L F AW G APL+ + + P S K P+ L + H
Sbjct: 36 LSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQ--YPMSQEARLG------IKPH 87
Query: 480 IQEMLETGVLKRLDSTTGFLSRLFLVPK-GNGGTRPVLNLKGLNQFLSPKKFSLINHFRI 538
IQ +L+ G+L + + + + L V K G RPV +L+ +N+ + ++ N + +
Sbjct: 88 IQRLLDQGIL--VPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNL 145
Query: 539 PSFLQKG-DYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAM------TCLPFGLATA 591
S L + +DL A+F + + T Q A + + + T LP G +
Sbjct: 146 LSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNS 205
Query: 592 PQAF-ASLSNWVASL-LRSRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F +L +A ++ + ++ Y+DD LL + + + + LG+LG+ +
Sbjct: 206 PTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSEQDCQRGTRALLQTLGNLGYRAS 265
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTL 685
+K+ + V ++LG + + WL E ++ T+
Sbjct: 266 AKKAQICQKQV-KYLGYLLKE--GQRWLTEARKETV 298
>pdb|4B3P|A Chain A, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique
Rt Conformation And Substrate Interface
Length = 560
Score = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 63/279 (22%), Positives = 118/279 (42%), Gaps = 38/279 (13%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRI-- 538
EM + G + ++ + + +F + K +G R +++ + LN KK ++
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDGTKWRKLVDFRELN-----KKTQDFWEVQLGI 94
Query: 539 --PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLA 589
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G
Sbjct: 95 PHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWK 154
Query: 590 TAPQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWI 647
+P F S + R + +V+ Y+DD L V D I + + K+ L W
Sbjct: 155 GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWG 213
Query: 648 VNLQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLL 707
+ P FL + ++ H D+ T+ I+ L +W ++ + L+
Sbjct: 214 LTTPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLV 261
Query: 708 GYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
G L++AS + P ++++ LLR G LT + P
Sbjct: 262 GKLNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|4B3O|A Chain A, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique
Rt Conformation And Substrate Interface
Length = 560
Score = 44.7 bits (104), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 63/279 (22%), Positives = 118/279 (42%), Gaps = 38/279 (13%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRI-- 538
EM + G + ++ + + +F + K +G R +++ + LN KK ++
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDGTKWRKLVDFRELN-----KKTQDFWEVQLGI 94
Query: 539 --PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLA 589
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G
Sbjct: 95 PHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWK 154
Query: 590 TAPQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWI 647
+P F S + R + +V+ Y+DD L V D I + + K+ L W
Sbjct: 155 GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWG 213
Query: 648 VNLQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLL 707
+ P FL + ++ H D+ T+ I+ L +W ++ + L+
Sbjct: 214 LTTPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLV 261
Query: 708 GYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
G L++AS + P ++++ LLR G LT + P
Sbjct: 262 GKLNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|4B3Q|A Chain A, Structures Of Hiv-1 Rt And Rna-dna Complex Reveal A Unique
Rt Conformation And Substrate Interface
Length = 560
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 63/279 (22%), Positives = 118/279 (42%), Gaps = 38/279 (13%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRI-- 538
EM + G + ++ + + +F + K +G R +++ + LN KK ++
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDGTKWRKLVDFRELN-----KKTQDFWEVQLGI 94
Query: 539 --PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLA 589
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G
Sbjct: 95 PHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWK 154
Query: 590 TAPQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWI 647
+P F S + R + +V+ Y+DD L V D I + + K+ L W
Sbjct: 155 GSPAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWG 213
Query: 648 VNLQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLL 707
+ P FL + ++ H D+ T+ I+ L +W ++ + L+
Sbjct: 214 LTTPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLV 261
Query: 708 GYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
G L++AS + P ++++ LLR G LT + P
Sbjct: 262 GKLNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1HNI|B Chain B, Structure Of Hiv-1 Reverse Transcriptase In A Complex With
The Nonnucleoside Inhibitor Alpha-Apa R 95845 At 2.8
Angstroms Resolution
Length = 427
Score = 43.9 bits (102), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 61/275 (22%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++ RQ S L G LT + P
Sbjct: 266 WASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1RT3|B Chain B, Azt Drug Resistant Hiv-1 Reverse Transcriptase Complexed
With 1051u91
Length = 440
Score = 43.5 bits (101), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 61/275 (22%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K N R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKNSTRWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1T05|B Chain B, Hiv-1 Reverse Transcriptase Crosslinked To Template-Primer
With Tenofovir-Diphosphate Bound As The Incoming
Nucleotide Substrate
Length = 437
Score = 43.1 bits (100), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 61/275 (22%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++ RQ S L G LT + P
Sbjct: 266 WASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1BQN|A Chain A, Tyr 188 Leu Hiv-1 RtHBY 097
Length = 558
Score = 43.1 bits (100), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 53/217 (24%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD LLV D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LLVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPQKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|3KJV|B Chain B, Hiv-1 Reverse Transcriptase In Complex With Dna
pdb|3KK1|B Chain B, Hiv-1 Reverse Transcriptase-Dna Complex With Nuceotide
Inhibitor Gs- 9148-Diphosphate Bound In Nucleotide Site
pdb|3KK2|B Chain B, Hiv-1 Reverse Transcriptase-Dna Complex With Datp Bound In
The Nucleotide Binding Site
pdb|3KK3|B Chain B, Hiv-1 Reverse Transcriptase-Dna Complex With Gs-9148
Terminated Primer
Length = 452
Score = 43.1 bits (100), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 53/217 (24%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 109 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 168
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 169 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 227
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 228 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 275
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 276 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 306
>pdb|2YNF|A Chain A, Hiv-1 Reverse Transcriptase Y188l Mutant In Complex With
Inhibitor Gsk560
Length = 563
Score = 43.1 bits (100), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 53/217 (24%), Positives = 93/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 100 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 159
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD LLV D I + + K+ L W +
Sbjct: 160 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LLVGSDLEIGQHRTKIEELRQHLLRWGLT 218
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 219 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 266
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 267 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 297
>pdb|2IAJ|B Chain B, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse
Transcriptase (Rt) In Complex With Atp
pdb|2IC3|B Chain B, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse
Transcriptase (Rt) In Complex With Nonnucleoside
Inhibitor Hby 097
Length = 447
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++ RQ S L G LT + P
Sbjct: 266 WASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1FKO|B Chain B, Crystal Structure Of Nnrti Resistant K103n Mutant Hiv-1
Reverse Transcriptase In Complex With Dmp-266(Efavirenz)
pdb|1FKP|B Chain B, Crystal Structure Of Nnrti Resistant K103n Mutant Hiv-1
Reverse Transcriptase In Complex With Nevirapine
pdb|3DM2|B Chain B, Crystal Structure Of Hiv-1 K103n Mutant Reverse
Transcriptase In Complex With Gw564511.
pdb|3DOK|B Chain B, Crystal Structure Of K103n Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw678248.
pdb|3MED|B Chain B, Hiv-1 K103n Reverse Transcriptase In Complex With Tmc125
pdb|3MEG|B Chain B, Hiv-1 K103n Reverse Transcriptase In Complex With Tmc278
pdb|2WOM|B Chain B, Crystal Structure Of Uk-453061 Bound To Hiv-1 Reverse
Transcriptase (K103n)
Length = 440
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1HPZ|B Chain B, Human Immunodeficiency Virus Type 1
pdb|1HQE|B Chain B, Human Immunodeficiency Virus Type 1
pdb|1HQU|B Chain B, Human Immunodeficiency Virus Type 1
pdb|1SV5|B Chain B, Crystal Structure Of K103n Mutant Hiv-1 Reverse
Transcriptase (Rt) In Complex With Janssen-R165335
Length = 430
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 265 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1JKH|B Chain B, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Dmp-266(Efavirenz)
pdb|1JLA|B Chain B, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Tnk-651
pdb|1JLB|B Chain B, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1JLC|B Chain B, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Pett-2
Length = 440
Score = 42.7 bits (99), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1UWB|B Chain B, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo
Length = 427
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++ RQ S L G LT + P
Sbjct: 266 WASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|3DRS|B Chain B, Hiv Reverse Transcriptase K103n Mutant In Complex With
Inhibitor R8d
pdb|3LP0|B Chain B, Hiv-1 Reverse Transcriptase With Inhibitor
pdb|3LP1|B Chain B, Hiv-1 Reverse Transcriptase With Inhibitor
pdb|3LP2|B Chain B, Hiv-1 Reverse Transcriptase With Inhibitor
pdb|3TAM|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (K103n
Mutant) In Complex With Inhibitor M06
Length = 443
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 43 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 101
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 102 GLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 161
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 162 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 220
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 221 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 268
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 269 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 297
>pdb|3DRR|B Chain B, Hiv Reverse Transcriptase Y181c Mutant In Complex With
Inhibitor R8e
Length = 443
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 43 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 101
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 102 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 161
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 162 IFQSSMTKILEPFRKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 220
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 221 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 268
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 269 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 297
>pdb|1HYS|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With A Polypurine Tract Rna:dna
Length = 425
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++ RQ S L G LT + P
Sbjct: 266 WASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|2HND|B Chain B, Crystal Structure Of K101e Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 422
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 34 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 92
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 93 GLEKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 152
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 153 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 211
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 212 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 259
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 260 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 288
>pdb|1JLE|B Chain B, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase
pdb|1JLF|B Chain B, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1JLG|B Chain B, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase In Complex With Uc-781
Length = 440
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LCVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2ZD1|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt
Inhibitor
pdb|2ZE2|B Chain B, Crystal Structure Of L100iK103N MUTANT HIV-1 Reverse
Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine),
A Non-Nucleoside Rt Inhibitor
pdb|3BGR|B Chain B, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse
Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine),
A Non-Nucleoside Rt Inhibitor
pdb|3IG1|B Chain B, Hiv-1 Reverse Transcriptase With The Inhibitor Beta-
Thujaplicinol Bound At The Rnase H Active Site
pdb|3IRX|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With The Non-Nucleoside Rt Inhibitor
(E)-S-Methyl
5-(1-(3,7-Dimethyl-2-Oxo-2,
3-Dihydrobenzo[d]oxazol-5-Yl)-5-
(5-Methyl-1,3,4-Oxadiazol-2-Yl)pent-1-Enyl)-2-Methoxy-3-
Methylbenzothioate.
pdb|3IS9|B Chain B, Crystal Structure Of The Hiv-1 Reverse Transcriptase (Rt)
In Complex With The Alkenyldiarylmethane (Adam)
Non-Nucleoside Rt Inhibitor Dimethyl
3,3'-(6-Methoxy-6-Oxohex-1-Ene-1,1-
Diyl)bis(5-Cyano-6-Methoxybenzoate).
pdb|3QO9|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Tsao-T, A Non-Nucleoside Rt Inhibitor
(Nnrti)
pdb|2YKM|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With A Difluoromethylbenzoxazole (Dfmb)
Pyrimidine Thioether Derivative, A Non-Nucleoside Rt
Inhibitor (Nnrti)
pdb|2YKN|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With A Difluoromethylbenzoxazole (Dfmb)
Pyrimidine Thioether Derivative, A Non-Nucleoside Rt
Inhibitor (Nnrti)
pdb|3V4I|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Dna And Azttp
pdb|3V4I|D Chain D, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Dna And Azttp
pdb|3V6D|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt)
Cross-Linked With Azt-Terminated Dna
pdb|3V6D|D Chain D, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt)
Cross-Linked With Azt-Terminated Dna
pdb|3V81|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Dna And The Nonnucleoside Inhibitor Nevirapine
pdb|3V81|D Chain D, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Dna And The Nonnucleoside Inhibitor Nevirapine
pdb|4H4M|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With (E)-
3-(3-Chloro-5-(4-Chloro-2-(2-(2,4-Dioxo-3,4-
Dihydropyrimidin-1(2h)-
Yl)ethoxy)phenoxy)phenyl)acrylonitrile (Jlj494), A
Non-Nucleoside Inhibitor
pdb|4H4O|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With
(E)-3-(3-(2-(2-(2,4-Dioxo-3,
4-Dihydropyrimidin-1(2h)-Yl)ethoxy)- 4-
Fluorophenoxy)-5-Fluorophenyl)acrylonitrile (Jlj506), A
Non- Nucleoside Inhibitor
pdb|4I2P|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Rilpivirine (tmc278) Based Analogue
pdb|4I2Q|B Chain B, Crystal Structure Of K103n/y181c Mutant Of Hiv-1 Reverse
Transcriptase In Complex With Rilpivirine (tmc278)
Analogue
pdb|4G1Q|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (rt) In
Complex With Rilpivirine (tmc278, Edurant), A
Non-nucleoside Rt-inhibiting Drug
Length = 428
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 265 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|3DLK|B Chain B, Crystal Structure Of An Engineered Form Of The Hiv-1
Reverse Transcriptase, Rt69a
pdb|3QLH|B Chain B, Hiv-1 Reverse Transcriptase In Complex With Manicol At The
Rnase H Active Site And Tmc278 (rilpivirine) At The
Nnrti Binding Pocket
Length = 423
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 35 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 92
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 93 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 152
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 153 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 211
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 212 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 259
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 260 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 289
>pdb|2OPR|B Chain B, Crystal Structure Of K101e Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw420867x
Length = 426
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 35 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 93
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 94 GLEKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 153
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 154 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 212
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 213 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 260
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 261 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 289
>pdb|1HNV|B Chain B, Structure Of Hiv-1 Rt(Slash)tibo R 86183 Complex Reveals
Similarity In The Binding Of Diverse Nonnucleoside
Inhibitors
pdb|1DLO|B Chain B, Human Immunodeficiency Virus Type 1
pdb|1TVR|B Chain B, Hiv-1 Rt9-Cl Tibo
pdb|4DG1|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Polymorphism Mutation K172a And K173a
Length = 427
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++ RQ S L G LT + P
Sbjct: 266 WASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|4I7G|B Chain B, Hiv-1 Reverse Transcriptase With Bound Fragment At Nnrti
Adjacent Site
pdb|4ICL|B Chain B, Hiv-1 Reverse Transcriptase With Bound Fragment At The
Incoming Dntp Binding Site
pdb|4ID5|B Chain B, Hiv-1 Reverse Transcriptase With Bound Fragment At The
Rnase H Primer Grip Site
pdb|4IDK|B Chain B, Hiv-1 Reverse Transcriptase With Bound Fragment At The 428
Site
pdb|4IFV|B Chain B, Detecting Allosteric Sites Of Hiv-1 Reverse Transcriptase
By X-ray Crystallographic Fragment Screening
pdb|4IFY|B Chain B, Hiv-1 Reverse Transcriptase With Bound Fragment At The
Knuckles Site
pdb|4IG0|B Chain B, Hiv-1 Reverse Transcriptase With Bound Fragment At The 507
Site
pdb|4IG3|B Chain B, Hiv-1 Reverse Transcriptase With Bound Fragment Near
Knuckles Site
Length = 429
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 41 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 98
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 158
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 217
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 218 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 265
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 266 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 295
>pdb|1QAI|A Chain A, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1QAI|B Chain B, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1MML|A Chain A, Mechanistic Implications From The Structure Of A Catalytic
Fragment Of Mmlv Reverse Transcriptase
Length = 265
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/262 (22%), Positives = 109/262 (41%), Gaps = 35/262 (13%)
Query: 426 LRRFVDAWIRLGA------PAPLVRIVSGYAIPFSAKPPLVPLCSLQHLATPVSSAMSL- 478
L F AW G APL+ + + P S K P+S L
Sbjct: 17 LSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIK------------QYPMSQEARLG 64
Query: 479 ---HIQEMLETGVLKRLDSTTGFLSRLFLVPK-GNGGTRPVLNLKGLNQFLSPKKFSLIN 534
HIQ +L+ G+L + + + + L V K G RPV +L+ +N+ + ++ N
Sbjct: 65 IKPHIQRLLDQGIL--VPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPN 122
Query: 535 HFRIPSFLQKG-DYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAM------TCLPFG 587
+ + S L + +DL A+F + + T Q A + + + T LP G
Sbjct: 123 PYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQG 182
Query: 588 LATAPQAF-ASLSNWVASL-LRSRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLG 645
+P F +L +A ++ + ++ Y+DD LL + + + LG+LG
Sbjct: 183 FKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLG 242
Query: 646 WIVNLQKSSLSPAPVLQFLGIM 667
+ + +K+ + V ++LG +
Sbjct: 243 YRASAKKAQICQKQV-KYLGYL 263
>pdb|1RTH|B Chain B, High Resolution Structures Of Hiv-1 Rt From Four Rt-
Inhibitor Complexes
pdb|1RTI|B Chain B, High Resolution Structures Of Hiv-1 Rt From Four Rt-
Inhibitor Complexes
pdb|1RTJ|B Chain B, Mechanism Of Inhibition Of Hiv-1 Reverse Transcriptase By
Non-Nucleoside Inhibitors
pdb|1VRT|B Chain B, High Resolution Structures Of Hiv-1 Rt From Four Rt-
Inhibitor Complexes
pdb|1VRU|B Chain B, High Resolution Structures Of Hiv-1 Rt From Four Rt-
Inhibitor Complexes
pdb|1REV|B Chain B, Hiv-1 Reverse Transcriptase
pdb|1RT2|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase Complexed
With Tnk-651
pdb|1RT1|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase Complexed
With Mkc-442
pdb|1KLM|B Chain B, Hiv-1 Reverse Transcriptase Complexed With Bhap U-90152
pdb|1RT4|B Chain B, Hiv-1 Reverse Transcriptase Complexed With Uc781
pdb|1RT5|B Chain B, Hiv-1 Reverse Transcriptase Complexed With Uc10
pdb|1RT6|B Chain B, Hiv-1 Reverse Transcriptase Complexed With Uc38
pdb|1RT7|B Chain B, Hiv-1 Reverse Transcriptase Complexed With Uc84
pdb|1RTD|B Chain B, Structure Of A Catalytic Complex Of Hiv-1 Reverse
Transcriptase: Implications For Nucleoside Analog Drug
Resistance
pdb|1RTD|D Chain D, Structure Of A Catalytic Complex Of Hiv-1 Reverse
Transcriptase: Implications For Nucleoside Analog Drug
Resistance
pdb|1DTT|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Pett-2 (Pett130a94)
pdb|1DTQ|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Pett-1 (Pett131a94)
pdb|1C1C|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Tnk-6123
pdb|1C0T|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Bm+21.1326
pdb|1C0U|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Bm+50.0934
pdb|1EP4|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With S-1153
pdb|1FK9|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Dmp- 266(Efavirenz)
pdb|1JLQ|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With 739w94
pdb|1TKT|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw426318
pdb|1TKX|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw490745
pdb|1TKZ|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw429576
pdb|1TL1|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw451211
pdb|1TL3|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw450557
pdb|2RKI|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With A Triazole Derived Nnrti
pdb|3DLE|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gf128590.
pdb|3DLG|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw564511.
pdb|3DOL|B Chain B, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw695634.
pdb|3DI6|B Chain B, Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor
pdb|3DYA|B Chain B, Hiv-1 Rt With Non-Nucleoside Inhibitor Annulated Pyrazole
1
pdb|3E01|B Chain B, Hiv-Rt With Non-Nucleoside Inhibitor Annulated Pyrazole 2
pdb|3MEC|B Chain B, Hiv-1 Reverse Transcriptase In Complex With Tmc125
pdb|3MEE|B Chain B, Hiv-1 Reverse Transcriptase In Complex With Tmc278
pdb|3M8P|B Chain B, Hiv-1 Rt With Nnrti Tmc-125
pdb|3M8Q|B Chain B, Hiv-1 Rt With Aminopyrimidine Nnrti
pdb|2WON|B Chain B, Crystal Structure Of Uk-453061 Bound To Hiv-1 Reverse
Transcriptase (Wild-Type).
pdb|3NBP|B Chain B, Hiv-1 Reverse Transcriptase With Aminopyrimidine Inhibitor
2
pdb|3QIP|B Chain B, Structure Of Hiv-1 Reverse Transcriptase In Complex With
An Rnase H Inhibitor And Nevirapine
pdb|4I7F|B Chain B, Hiv-1 Reverse Transcriptase In Complex With A Phosphonate
Analog Of Nevirapine
Length = 440
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1D1U|A Chain A, Use Of An N-Terminal Fragment From Moloney Murine Leukemia
Virus Reverse Transcriptase To Facilitate
Crystallization And Analysis Of A Pseudo-16-Mer Dna
Molecule Containing G- A Mispairs
pdb|1N4L|A Chain A, A Dna Analogue Of The Polypurine Tract Of Hiv-1
pdb|1ZTT|A Chain A, Netropsin Bound To D(cttaattcgaattaag) In Complex With
Mmlv Rt Catalytic Fragment
pdb|1ZTW|A Chain A, D(Cttaattcgaattaag) Complexed With Moloney Murine Leukemia
Virus Reverse Transcriptase Catalytic Fragment
pdb|2FJV|A Chain A, Rt29 Bound To D(Cttaattcgaattaag) In Complex With Mmlv Rt
Catalytic Fragment
pdb|2FJW|A Chain A, D(Cttgaatgcattcaag) In Complex With Mmlv Rt Catalytic
Fragment
pdb|2FJX|A Chain A, Rt29 Bound To D(Cttgaatgcattcaag) In Complex With Mmlv Rt
Catalytic Fragment
pdb|2FVP|A Chain A, A Structural Study Of The Ca Dinucleotide Step In The
Integrase Processing Site Of Moloney Murine Leukemia
Virus
pdb|2FVQ|A Chain A, A Structural Study Of The Ca Dinucleotide Step In The
Integrase Processing Site Of Moloney Murine Leukemia
Virus
pdb|2FVR|A Chain A, A Structural Study Of The Ca Dinucleotide Step In The
Integrase Processing Site Of Moloney Murine Leukemia
Virus
pdb|2FVS|A Chain A, A Structural Study Of The Ca Dinucleotide Step In The
Integrase Processing Site Of Moloney Murine Leukemia
Virus
pdb|2R2R|A Chain A, D(Attagttataactaat) Complexed With Mmlv Rt Catalytic
Fragment
pdb|2R2S|A Chain A, Co(Iii)bleomycinb2 Bound To D(Attagttataactaat) Complexed
With Mmlv Rt Catalytic Fragment
pdb|2R2T|A Chain A, D(Atttagttaactaaat) Complexed With Mmlv Rt Catalytic
Fragment
pdb|2R2U|A Chain A, Co(Iii)bleomycinb2 BithiazoleC-Terminal Tail Domain Bound
To D(Atttagttaactaaat) Complexed With Mmlv Rt Catalytic
Fragment
pdb|3FSI|A Chain A, Crystal Structure Of A Trypanocidal 4,4'-
Bis(Imidazolinylamino)diphenylamine Bound To Dna
Length = 255
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/262 (22%), Positives = 109/262 (41%), Gaps = 35/262 (13%)
Query: 426 LRRFVDAWIRLGA------PAPLVRIVSGYAIPFSAKPPLVPLCSLQHLATPVSSAMSL- 478
L F AW G APL+ + + P S K P+S L
Sbjct: 3 LSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIK------------QYPMSQEARLG 50
Query: 479 ---HIQEMLETGVLKRLDSTTGFLSRLFLVPK-GNGGTRPVLNLKGLNQFLSPKKFSLIN 534
HIQ +L+ G+L + + + + L V K G RPV +L+ +N+ + ++ N
Sbjct: 51 IKPHIQRLLDQGIL--VPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPN 108
Query: 535 HFRIPSFLQKG-DYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAM------TCLPFG 587
+ + S L + +DL A+F + + T Q A + + + T LP G
Sbjct: 109 PYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQG 168
Query: 588 LATAPQAF-ASLSNWVASL-LRSRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLG 645
+P F +L +A ++ + ++ Y+DD LL + + + LG+LG
Sbjct: 169 FKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLG 228
Query: 646 WIVNLQKSSLSPAPVLQFLGIM 667
+ + +K+ + V ++LG +
Sbjct: 229 YRASAKKAQICQKQV-KYLGYL 249
>pdb|1QE1|B Chain B, Crystal Structure Of 3tc-Resistant M184i Mutant Of Hiv-1
Reverse Transcriptase
Length = 427
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYIDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++ RQ S L G LT + P
Sbjct: 266 WASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|2IAJ|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse
Transcriptase (Rt) In Complex With Atp
pdb|2IC3|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse
Transcriptase (Rt) In Complex With Nonnucleoside
Inhibitor Hby 097
Length = 560
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|2HMI|B Chain B, Hiv-1 Reverse TranscriptaseFRAGMENT OF FAB 28DNA COMPLEX
pdb|1BQM|B Chain B, Hiv-1 RtHBY 097
pdb|1N5Y|B Chain B, Hiv-1 Reverse Transcriptase Crosslinked To Post-
Translocation Aztmp-Terminated Dna (Complex P)
pdb|1N6Q|B Chain B, Hiv-1 Reverse Transcriptase Crosslinked To Pre-
Translocation Aztmp-Terminated Dna (Complex N)
pdb|1S6P|B Chain B, Crystal Structure Of Human Immunodeficiency Virus Type 1
Reverse Transcriptase (Rt) In Complex With
Janssen-R100943
pdb|1S6Q|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R147681
pdb|1S9E|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R129385
pdb|1S9G|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R120394.
pdb|1SUQ|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R185545
pdb|2B6A|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Thr-50
pdb|2B5J|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R165481
pdb|2BAN|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R157208
pdb|2BE2|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With R221239
Length = 430
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 265 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1J5O|B Chain B, Crystal Structure Of Met184ile Mutant Of Hiv-1 Reverse
Transcriptase In Complex With Double Stranded Dna
Template- Primer
Length = 430
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYIDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 265 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1R0A|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase
Covalently Tethered To Dna Template-primer Solved To 2.8
Angstroms
pdb|2I5J|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Dhbnh, An Rnase H Inhibitor
Length = 429
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 265 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|3FFI|B Chain B, Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor
Length = 441
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 117/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 41 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 98
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 158
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 AIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 217
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 218 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 265
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++++ LLR G LT + P
Sbjct: 266 NWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 295
>pdb|2OPS|B Chain B, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw420867x
Length = 435
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 117/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 35 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 92
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 93 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 152
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 153 AIFQSSMTKILEPFRKQNPDIVIYQYMDD-LCVGSDLEIGQHRTKIEELRQHLLRWGLTT 211
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 212 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 259
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++++ LLR G LT + P
Sbjct: 260 NWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 289
>pdb|1T03|B Chain B, Hiv-1 Reverse Transcriptase Crosslinked To Tenofovir
Terminated Template-Primer (Complex P)
pdb|3JSM|B Chain B, K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To
Ds-Dna And Complexed With Tenofovir-Diphosphate As The
Incoming Nucleotide Substrate
pdb|3JYT|B Chain B, K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To
Ds- Dna And Complexed With Datp As The Incoming
Nucleotide Substrate
Length = 437
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++ RQ S L G LT + P
Sbjct: 266 WASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1RT3|A Chain A, Azt Drug Resistant Hiv-1 Reverse Transcriptase Complexed
With 1051u91
Length = 560
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 64/278 (23%), Positives = 116/278 (41%), Gaps = 36/278 (12%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K N R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKNSTRWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGW--IV 648
F S + R + +V+ Y+DD L V D I + + K+ L W
Sbjct: 158 AIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLFT 216
Query: 649 NLQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLG 708
QK P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 217 PDQKHQKEPP----FLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVG 262
Query: 709 YLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 263 KLNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|1I6J|A Chain A, Crystal Structure Of A Pseudo-16-Mer Dna With Stacked
Guanines And Two G-A Mispairs Complexed With The N-
Terminal Fragment Of Moloney Murine Leukemia Virus
Reverse Transcriptase
Length = 256
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/262 (22%), Positives = 109/262 (41%), Gaps = 35/262 (13%)
Query: 426 LRRFVDAWIRLGA------PAPLVRIVSGYAIPFSAKPPLVPLCSLQHLATPVSSAMSL- 478
L F AW G APL+ + + P S K P+S L
Sbjct: 4 LSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIK------------QYPMSQEARLG 51
Query: 479 ---HIQEMLETGVLKRLDSTTGFLSRLFLVPK-GNGGTRPVLNLKGLNQFLSPKKFSLIN 534
HIQ +L+ G+L + + + + L V K G RPV +L+ +N+ + ++ N
Sbjct: 52 IKPHIQRLLDQGIL--VPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPN 109
Query: 535 HFRIPSFLQKG-DYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAM------TCLPFG 587
+ + S L + +DL A+F + + T Q A + + + T LP G
Sbjct: 110 PYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQG 169
Query: 588 LATAPQAF-ASLSNWVASL-LRSRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLG 645
+P F +L +A ++ + ++ Y+DD LL + + + LG+LG
Sbjct: 170 FKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLG 229
Query: 646 WIVNLQKSSLSPAPVLQFLGIM 667
+ + +K+ + V ++LG +
Sbjct: 230 YRASAKKAQICQKQV-KYLGYL 250
>pdb|1D0E|A Chain A, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1D0E|B Chain B, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1QAJ|A Chain A, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
pdb|1QAJ|B Chain B, Crystal Structures Of The N-Terminal Fragment From Moloney
Murine Leukemia Virus Reverse Transcriptase Complexed
With Nucleic Acid: Functional Implications For
Template-Primer Binding To The Fingers Domain
Length = 259
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/262 (22%), Positives = 109/262 (41%), Gaps = 35/262 (13%)
Query: 426 LRRFVDAWIRLGA------PAPLVRIVSGYAIPFSAKPPLVPLCSLQHLATPVSSAMSL- 478
L F AW G APL+ + + P S K P+S L
Sbjct: 7 LSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIK------------QYPMSQEARLG 54
Query: 479 ---HIQEMLETGVLKRLDSTTGFLSRLFLVPK-GNGGTRPVLNLKGLNQFLSPKKFSLIN 534
HIQ +L+ G+L + + + + L V K G RPV +L+ +N+ + ++ N
Sbjct: 55 IKPHIQRLLDQGIL--VPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPN 112
Query: 535 HFRIPSFLQKG-DYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAM------TCLPFG 587
+ + S L + +DL A+F + + T Q A + + + T LP G
Sbjct: 113 PYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQG 172
Query: 588 LATAPQAF-ASLSNWVASL-LRSRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLG 645
+P F +L +A ++ + ++ Y+DD LL + + + LG+LG
Sbjct: 173 FKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLG 232
Query: 646 WIVNLQKSSLSPAPVLQFLGIM 667
+ + +K+ + V ++LG +
Sbjct: 233 YRASAKKAQICQKQV-KYLGYL 253
>pdb|3KLE|B Chain B, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To A Dsdna With A Bound
Excision Product, Aztppppa
pdb|3KLE|F Chain F, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To A Dsdna With A Bound
Excision Product, Aztppppa
pdb|3KLE|J Chain J, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To A Dsdna With A Bound
Excision Product, Aztppppa
pdb|3KLE|N Chain N, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To A Dsdna With A Bound
Excision Product, Aztppppa
pdb|3KLG|B Chain B, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To Pre-Translocation
Aztmp-Terminated Dna (Complex N)
pdb|3KLG|F Chain F, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To Pre-Translocation
Aztmp-Terminated Dna (Complex N)
pdb|3KLH|B Chain B, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To Post-Translocation
Aztmp-Terminated Dna (Complex P)
pdb|3KLI|B Chain B, Crystal Structure Of Unliganded Azt-Resistant Hiv-1
Reverse Transcriptase
Length = 437
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 265 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1UWB|A Chain A, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo
Length = 558
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|2RF2|B Chain B, Hiv Reverse Transcriptase In Complex With Inhibitor 7e
(Nnrti)
pdb|3C6T|B Chain B, Crystal Structure Of Hiv Reverse Transcriptase In Complex
With Inhibitor 14
pdb|3C6U|B Chain B, Crystal Structure Of Hiv Reverse Transcriptase In Complex
With Inhibitor 22
pdb|3DRP|B Chain B, Hiv Reverse Transcriptase In Complex With Inhibitor R8e
pdb|3I0R|B Chain B, Crystal Structure Of Hiv Reverse Transcriptase In Complex
With Inhibitor 3
pdb|3I0S|B Chain B, Crystal Structure Of Hiv Reverse Transcriptase In Complex
With Inhibitor 7
Length = 443
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 43 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 101
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 102 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 161
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 162 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 220
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 221 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 268
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 269 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 297
>pdb|1HPZ|A Chain A, Human Immunodeficiency Virus Type 1
pdb|1HQE|A Chain A, Human Immunodeficiency Virus Type 1
pdb|1HQU|A Chain A, Human Immunodeficiency Virus Type 1
pdb|1SV5|A Chain A, Crystal Structure Of K103n Mutant Hiv-1 Reverse
Transcriptase (Rt) In Complex With Janssen-R165335
Length = 560
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1S1X|B Chain B, Crystal Structure Of V108i Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 440
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTILDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2YNF|B Chain B, Hiv-1 Reverse Transcriptase Y188l Mutant In Complex With
Inhibitor Gsk560
pdb|2YNG|B Chain B, Hiv-1 Reverse Transcriptase Mutant In Complex With
Inhibitor Gsk560
pdb|2YNH|B Chain B, Hiv-1 Reverse Transcriptase Mutant In Complex With
Inhibitor Gsk500
pdb|2YNI|B Chain B, Hiv-1 Reverse Transcriptase Mutant In Complex With
Inhibitor Gsk952
Length = 447
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 59 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 117
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 118 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 177
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 178 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 236
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 237 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 284
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 285 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 313
>pdb|1RW3|A Chain A, The Crystal Structure Of The Monomeric Reverse
Transcriptase From Moloney Murine Leukemia Virus
Length = 455
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 63/276 (22%), Positives = 117/276 (42%), Gaps = 29/276 (10%)
Query: 426 LRRFVDAWIRLGA------PAPLVRIVSGYAIPFSAKPPLVPLCSLQHLATPVSSAMSLH 479
L F AW G APL+ + + P S K P+ L + H
Sbjct: 7 LSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIK--QYPMSQEARLG------IKPH 58
Query: 480 IQEMLETGVLKRLDSTTGFLSRLFLVPK-GNGGTRPVLNLKGLNQFLSPKKFSLINHFRI 538
IQ +L+ G+L + + + + L V K G RPV +L+ +N+ + ++ N + +
Sbjct: 59 IQRLLDQGIL--VPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNL 116
Query: 539 PSFLQKG-DYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAM------TCLPFGLATA 591
S L + +DL A+F + + T Q A + + + T LP G +
Sbjct: 117 LSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQGFKNS 176
Query: 592 PQAF-ASLSNWVASL-LRSRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F +L +A ++ + ++ Y+DD LL + + + LG+LG+ +
Sbjct: 177 PTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLGYRAS 236
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTL 685
+K+ + V ++LG + + WL E ++ T+
Sbjct: 237 AKKAQICQKQV-KYLGYLLKE--GQRWLTEARKETV 269
>pdb|1HNI|A Chain A, Structure Of Hiv-1 Reverse Transcriptase In A Complex With
The Nonnucleoside Inhibitor Alpha-Apa R 95845 At 2.8
Angstroms Resolution
pdb|1HNV|A Chain A, Structure Of Hiv-1 Rt(Slash)tibo R 86183 Complex Reveals
Similarity In The Binding Of Diverse Nonnucleoside
Inhibitors
pdb|1TVR|A Chain A, Hiv-1 Rt9-Cl Tibo
pdb|2HMI|A Chain A, Hiv-1 Reverse TranscriptaseFRAGMENT OF FAB 28DNA COMPLEX
Length = 558
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|2OPP|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw420867x
Length = 427
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 36 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 94
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 95 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 154
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 155 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 213
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 214 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 261
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 262 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 290
>pdb|1LWC|B Chain B, Crystal Structure Of M184v Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 440
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 117/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFRKQNPDIVIYQYVDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++++ LLR G LT + P
Sbjct: 265 NWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1HYS|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With A Polypurine Tract Rna:dna
Length = 553
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|2I5J|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Dhbnh, An Rnase H Inhibitor
Length = 552
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|3MED|A Chain A, Hiv-1 K103n Reverse Transcriptase In Complex With Tmc125
pdb|3MEG|A Chain A, Hiv-1 K103n Reverse Transcriptase In Complex With Tmc278
pdb|2WOM|A Chain A, Crystal Structure Of Uk-453061 Bound To Hiv-1 Reverse
Transcriptase (K103n)
Length = 560
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1FKO|A Chain A, Crystal Structure Of Nnrti Resistant K103n Mutant Hiv-1
Reverse Transcriptase In Complex With Dmp-266(Efavirenz)
pdb|1FKP|A Chain A, Crystal Structure Of Nnrti Resistant K103n Mutant Hiv-1
Reverse Transcriptase In Complex With Nevirapine
Length = 543
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|3KLF|B Chain B, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|F Chain F, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|J Chain J, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|N Chain N, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
Length = 444
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 56 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 113
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 114 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 173
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 174 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 232
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 233 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 280
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++ RQ S L G LT + P
Sbjct: 281 NWASQIYPGIKV------RQLSKLLRGTKALTEVIP 310
>pdb|3DMJ|B Chain B, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse
Transcriptase In Complex With Gw564511
Length = 440
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSATVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|3DRS|A Chain A, Hiv Reverse Transcriptase K103n Mutant In Complex With
Inhibitor R8d
pdb|3LP0|A Chain A, Hiv-1 Reverse Transcriptase With Inhibitor
pdb|3LP1|A Chain A, Hiv-1 Reverse Transcriptase With Inhibitor
pdb|3LP2|A Chain A, Hiv-1 Reverse Transcriptase With Inhibitor
pdb|3T1A|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (K103n
Mutant) In Complex With Inhibitor M05
pdb|3T1A|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (K103n
Mutant) In Complex With Inhibitor M05
pdb|3TAM|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (K103n
Mutant) In Complex With Inhibitor M06
Length = 563
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 100 PAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 159
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 160 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 218
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 219 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 266
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 267 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 297
>pdb|2YKN|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With A Difluoromethylbenzoxazole (Dfmb)
Pyrimidine Thioether Derivative, A Non-Nucleoside Rt
Inhibitor (Nnrti)
Length = 562
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 60/276 (21%), Positives = 118/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYSTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P L ++G ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEPPLLWMG--YELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++++ LLR G LT + P
Sbjct: 265 NWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1DLO|A Chain A, Human Immunodeficiency Virus Type 1
pdb|1BQM|A Chain A, Hiv-1 RtHBY 097
Length = 556
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1S6P|A Chain A, Crystal Structure Of Human Immunodeficiency Virus Type 1
Reverse Transcriptase (Rt) In Complex With
Janssen-R100943
pdb|1S6Q|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R147681
pdb|1S9E|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R129385
pdb|1S9G|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R120394.
pdb|1SUQ|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R185545
pdb|2B6A|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Thr-50
pdb|2B5J|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R165481
pdb|2BAN|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Janssen-R157208
pdb|2BE2|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With R221239
Length = 560
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1QE1|A Chain A, Crystal Structure Of 3tc-Resistant M184i Mutant Of Hiv-1
Reverse Transcriptase
pdb|1J5O|A Chain A, Crystal Structure Of Met184ile Mutant Of Hiv-1 Reverse
Transcriptase In Complex With Double Stranded Dna
Template- Primer
Length = 558
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYIDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|2HND|A Chain A, Crystal Structure Of K101e Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 534
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 94 PAGLEKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 153
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 154 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 212
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 213 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 260
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 261 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 291
>pdb|3DM2|A Chain A, Crystal Structure Of Hiv-1 K103n Mutant Reverse
Transcriptase In Complex With Gw564511.
pdb|3DOK|A Chain A, Crystal Structure Of K103n Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw678248
Length = 560
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|3DRR|A Chain A, Hiv Reverse Transcriptase Y181c Mutant In Complex With
Inhibitor R8e
Length = 563
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 100 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 159
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 160 PAIFQSSMTKILEPFRKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 218
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 219 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 266
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 267 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 297
>pdb|2OPR|A Chain A, Crystal Structure Of K101e Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw420867x
Length = 547
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 96 PAGLEKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 155
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 156 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 214
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 215 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 262
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 263 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 293
>pdb|1S1W|B Chain B, Crystal Structure Of V106a Mutant Hiv-1 Reverse
Transcriptase In Complex With Uc-781
Length = 440
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 116/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSATVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++++ LLR G LT + P
Sbjct: 265 NWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1BQN|B Chain B, Tyr 188 Leu Hiv-1 RtHBY 097
Length = 430
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 61/276 (22%), Positives = 118/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD LLV D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LLVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVEPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P +++ + LLR G LT + P
Sbjct: 265 NWASQIYP-----GIKVRALSKLLR-GTKALTEVIP 294
>pdb|1S1T|B Chain B, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Uc-781
pdb|1S1U|B Chain B, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1S1V|B Chain B, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Tnk-651
Length = 440
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 60/276 (21%), Positives = 117/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ ++K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGIKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++++ LLR G LT + P
Sbjct: 265 NWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1LW0|B Chain B, Crystal Structure Of T215y Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1LW2|B Chain B, Crystal Structure Of T215y Mutant Hiv-1 Reverse
Transcriptase In Complex With 1051u91
Length = 440
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLYTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|3DI6|A Chain A, Hiv-1 Rt With Pyridazinone Non-Nucleoside Inhibitor
pdb|3DYA|A Chain A, Hiv-1 Rt With Non-Nucleoside Inhibitor Annulated Pyrazole
1
pdb|3E01|A Chain A, Hiv-Rt With Non-Nucleoside Inhibitor Annulated Pyrazole 2
pdb|3M8P|A Chain A, Hiv-1 Rt With Nnrti Tmc-125
pdb|3M8Q|A Chain A, Hiv-1 Rt With Aminopyrimidine Nnrti
pdb|3NBP|A Chain A, Hiv-1 Reverse Transcriptase With Aminopyrimidine Inhibitor
2
Length = 561
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2RKI|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With A Triazole Derived Nnrti
pdb|3LAK|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With N1-Heterocycle Pyrimidinedione
Non-Nucleoside Inhibitor
pdb|3LAK|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With N1-Heterocycle Pyrimidinedione
Non-Nucleoside Inhibitor
pdb|3LAL|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With N1-Ethyl Pyrimidinedione Non-Nucleoside
Inhibitor
pdb|3LAL|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With N1-Ethyl Pyrimidinedione Non-Nucleoside
Inhibitor
pdb|3LAM|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With N1-Propyl Pyrimidinedione Non-Nucleoside
Inhibitor
pdb|3LAM|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With N1-Propyl Pyrimidinedione Non-Nucleoside
Inhibitor
pdb|3LAN|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With N1-Butyl Pyrimidinedione Non-Nucleoside
Inhibitor
pdb|3LAN|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With N1-Butyl Pyrimidinedione Non-Nucleoside
Inhibitor
pdb|3MEC|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Tmc125
pdb|3MEE|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Tmc278
pdb|2WON|A Chain A, Crystal Structure Of Uk-453061 Bound To Hiv-1 Reverse
Transcriptase (Wild-Type).
pdb|3QIP|A Chain A, Structure Of Hiv-1 Reverse Transcriptase In Complex With
An Rnase H Inhibitor And Nevirapine
pdb|4I7F|A Chain A, Hiv-1 Reverse Transcriptase In Complex With A Phosphonate
Analog Of Nevirapine
Length = 560
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1JKH|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Dmp-266(Efavirenz)
pdb|1JLA|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Tnk-651
pdb|1JLB|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1JLC|A Chain A, Crystal Structure Of Y181c Mutant Hiv-1 Reverse
Transcriptase In Complex With Pett-2
Length = 560
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|3FFI|A Chain A, Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor
Length = 561
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 98 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 157
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 216
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 217 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 264
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 265 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 295
>pdb|2OPP|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw420867x
Length = 542
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 94 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 153
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 154 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 212
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 213 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 260
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 261 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 291
>pdb|3KJV|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Dna
pdb|3KK1|A Chain A, Hiv-1 Reverse Transcriptase-Dna Complex With Nuceotide
Inhibitor Gs- 9148-Diphosphate Bound In Nucleotide Site
pdb|3KK2|A Chain A, Hiv-1 Reverse Transcriptase-Dna Complex With Datp Bound In
The Nucleotide Binding Site
pdb|3KK3|A Chain A, Hiv-1 Reverse Transcriptase-Dna Complex With Gs-9148
Terminated Primer
Length = 560
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 53/217 (24%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDICKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|2JLE|A Chain A, Novel Indazole Nnrtis Created Using Molecular Template
Hybridization Based On Crystallographic Overlays
pdb|2JLE|B Chain B, Novel Indazole Nnrtis Created Using Molecular Template
Hybridization Based On Crystallographic Overlays
Length = 566
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2RF2|A Chain A, Hiv Reverse Transcriptase In Complex With Inhibitor 7e
(Nnrti)
pdb|3C6T|A Chain A, Crystal Structure Of Hiv Reverse Transcriptase In Complex
With Inhibitor 14
pdb|3C6U|A Chain A, Crystal Structure Of Hiv Reverse Transcriptase In Complex
With Inhibitor 22
pdb|3DRP|A Chain A, Hiv Reverse Transcriptase In Complex With Inhibitor R8e
pdb|3I0R|A Chain A, Crystal Structure Of Hiv Reverse Transcriptase In Complex
With Inhibitor 3
pdb|3I0S|A Chain A, Crystal Structure Of Hiv Reverse Transcriptase In Complex
With Inhibitor 7
pdb|3T19|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Wild
Type) In Complex With Inhibitor M05
pdb|3T19|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase (Wild
Type) In Complex With Inhibitor M05
pdb|2YNG|A Chain A, Hiv-1 Reverse Transcriptase Mutant In Complex With
Inhibitor Gsk560
pdb|2YNH|A Chain A, Hiv-1 Reverse Transcriptase Mutant In Complex With
Inhibitor Gsk500
pdb|2YNI|A Chain A, Hiv-1 Reverse Transcriptase Mutant In Complex With
Inhibitor Gsk952
Length = 563
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 100 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 159
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 160 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 218
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 219 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 266
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 267 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 297
>pdb|1FK9|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Dmp- 266(Efavirenz)
Length = 543
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|1JLF|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LCVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|1LWE|B Chain B, Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse
Transcriptase (Rtmn) In Complex With Nevirapine
Length = 440
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLY 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2HNY|B Chain B, Crystal Structure Of E138k Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|2HNZ|B Chain B, Crystal Structure Of E138k Mutant Hiv-1 Reverse
Transcriptase In Complex With Pett-2
Length = 422
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 61/275 (22%), Positives = 116/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 34 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 92
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYN----GDVLAMTCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N G LP G +P
Sbjct: 93 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNKTPGIRYQYNVLPQGWKGSPA 152
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 153 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 211
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 212 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 259
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 260 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 288
>pdb|1IKV|B Chain B, K103n Mutant Hiv-1 Reverse Transcriptase In Complex With
Efivarenz
pdb|1IKX|B Chain B, K103n Mutant Hiv-1 Reverse Transcriptase In Complex With
The Inhibitor Pnu142721
pdb|1IKY|B Chain B, Hiv-1 Reverse Transcriptase In Complex With The Inhibitor
Msc194
Length = 427
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 59/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2OPS|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw420867x
Length = 542
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 96 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 155
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 156 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LCVGSDLEIGQHRTKIEELRQHLLRWGLT 214
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 215 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 262
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 263 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 293
>pdb|1REV|A Chain A, Hiv-1 Reverse Transcriptase
pdb|1RT2|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase Complexed
With Tnk-651
pdb|1RT1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase Complexed
With Mkc-442
pdb|1KLM|A Chain A, Hiv-1 Reverse Transcriptase Complexed With Bhap U-90152
pdb|1RT4|A Chain A, Hiv-1 Reverse Transcriptase Complexed With Uc781
pdb|1RT5|A Chain A, Hiv-1 Reverse Transcriptase Complexed With Uc10
pdb|1RT6|A Chain A, Hiv-1 Reverse Transcriptase Complexed With Uc38
pdb|1RT7|A Chain A, Hiv-1 Reverse Transcriptase Complexed With Uc84
pdb|1DTT|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Pett-2 (Pett130a94)
pdb|1DTQ|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Pett-1 (Pett131a94)
pdb|1C1B|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gca-186
pdb|1C1C|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Tnk-6123
pdb|1C0T|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Bm+21.1326
pdb|1C0U|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Bm+50.0934
pdb|1EP4|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With S-1153
pdb|1JLQ|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With 739w94
pdb|1TKT|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw426318
pdb|1TKX|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw490745
pdb|1TKZ|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw429576
pdb|1TL1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw451211
pdb|1TL3|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw450557
pdb|3DLE|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gf128590.
pdb|3DLG|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw564511.
pdb|1RTJ|A Chain A, Mechanism Of Inhibition Of Hiv-1 Reverse Transcriptase By
Non-Nucleoside Inhibitors
pdb|1RTI|A Chain A, High Resolution Structures Of Hiv-1 Rt From Four Rt-
Inhibitor Complexes
pdb|1VRT|A Chain A, High Resolution Structures Of Hiv-1 Rt From Four Rt-
Inhibitor Complexes
pdb|1RTH|A Chain A, High Resolution Structures Of Hiv-1 Rt From Four Rt-
Inhibitor Complexes
pdb|1VRU|A Chain A, High Resolution Structures Of Hiv-1 Rt From Four Rt-
Inhibitor Complexes
Length = 560
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|2OPQ|B Chain B, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw420867x
Length = 424
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 59/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 36 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 94
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
++K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 95 GIKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 154
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 155 IFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 213
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 214 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 261
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 262 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 290
>pdb|1LWF|B Chain B, Crystal Structure Of A Mutant Hiv-1 Reverse Transcriptase
(rtmq+m184v: M41l/d67n/k70r/m184v/t215y) In Complex With
Nevirapine
Length = 440
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 60/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
E+ + G + ++ + + +F + K N R +++ + LN+ + + + P+
Sbjct: 40 ELEKEGKISKIGPENPYNTPVFAIKKKNSTRWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFRKQNPDIVIYQYVDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLYTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1JLE|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase
pdb|1JLG|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase In Complex With Uc-781
Length = 560
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LXVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|1NND|A Chain A, Arginine 116 Is Essential For Nucleic Acid Recognition By
The Fingers Domain Of Moloney Murine Leukemia Virus
Reverse Transcriptase
Length = 255
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 60/262 (22%), Positives = 108/262 (41%), Gaps = 35/262 (13%)
Query: 426 LRRFVDAWIRLGA------PAPLVRIVSGYAIPFSAKPPLVPLCSLQHLATPVSSAMSL- 478
L F AW G APL+ + + P S K P+S L
Sbjct: 3 LSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIK------------QYPMSQEARLG 50
Query: 479 ---HIQEMLETGVLKRLDSTTGFLSRLFLVPK-GNGGTRPVLNLKGLNQFLSPKKFSLIN 534
HIQ +L+ G+L + + + + L V K G RPV +L +N+ + ++ N
Sbjct: 51 IKPHIQRLLDQGIL--VPCQSPWNTPLLPVKKPGTNDYRPVQDLAEVNKRVEDIHPTVPN 108
Query: 535 HFRIPSFLQKG-DYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAM------TCLPFG 587
+ + S L + +DL A+F + + T Q A + + + T LP G
Sbjct: 109 PYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPEMGISGQLTWTRLPQG 168
Query: 588 LATAPQAF-ASLSNWVASL-LRSRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLG 645
+P F +L +A ++ + ++ Y+DD LL + + + LG+LG
Sbjct: 169 FKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGNLG 228
Query: 646 WIVNLQKSSLSPAPVLQFLGIM 667
+ + +K+ + V ++LG +
Sbjct: 229 YRASAKKAQICQKQV-KYLGYL 249
>pdb|1EET|B Chain B, Hiv-1 Reverse Transcriptase In Complex With The Inhibitor
Msc204
pdb|1IKW|B Chain B, Wild Type Hiv-1 Reverse Transcriptase In Complex With
Efavirenz
pdb|3ISN|D Chain D, Crystal Structure Of Hiv-1 Rt Bound To A 6-Vinylpyrimidine
Inhibitor
pdb|3ITH|B Chain B, Crystal Structure Of The Hiv-1 Reverse Transcriptase Bound
To A 6-Vinylpyrimidine Inhibitor
pdb|3ITH|D Chain D, Crystal Structure Of The Hiv-1 Reverse Transcriptase Bound
To A 6-Vinylpyrimidine Inhibitor
Length = 427
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 59/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|3HVT|B Chain B, Structural Basis Of Asymmetry In The Human
Immunodeficiency Virus Type 1 Reverse Transcriptase
Heterodimer
pdb|2VG5|B Chain B, Crystal Structures Of Hiv-1 Reverse Transcriptase
Complexes With Thiocarbamate Non-Nucleoside Inhibitors
pdb|2VG6|B Chain B, Crystal Structures Of Hiv-1 Reverse Transcriptase
Complexes With Thiocarbamate Non-Nucleoside Inhibitors
pdb|2VG7|B Chain B, Crystal Structures Of Hiv-1 Reverse Transcriptase
Complexes With Thiocarbamate Non-Nucleoside Inhibitors
Length = 428
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 59/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1HMV|B Chain B, The Structure Of Unliganded Reverse Transcriptase From The
Human Immunodeficiency Virus Type 1
pdb|1TV6|B Chain B, Hiv-1 Reverse Transcriptase Complexed With Cp-94,707
pdb|1HMV|D Chain D, The Structure Of Unliganded Reverse Transcriptase From The
Human Immunodeficiency Virus Type 1
pdb|1HMV|F Chain F, The Structure Of Unliganded Reverse Transcriptase From The
Human Immunodeficiency Virus Type 1
pdb|1HMV|H Chain H, The Structure Of Unliganded Reverse Transcriptase From The
Human Immunodeficiency Virus Type 1
Length = 440
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 59/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P FL + ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1C1B|B Chain B, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gca-186
Length = 440
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 60/276 (21%), Positives = 117/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 40 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 97
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 98 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 157
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 216
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 217 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 264
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++++ LLR G LT + P
Sbjct: 265 NWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1S1X|A Chain A, Crystal Structure Of V108i Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTILDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|3BGR|A Chain A, Crystal Structure Of K103nY181C MUTANT HIV-1 Reverse
Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine),
A Non-Nucleoside Rt Inhibitor
pdb|4I2Q|A Chain A, Crystal Structure Of K103n/y181c Mutant Of Hiv-1 Reverse
Transcriptase In Complex With Rilpivirine (tmc278)
Analogue
Length = 557
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 99 PAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 158
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + ++ +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 PAIFQSSMTKILEPFAAQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 217
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 218 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 265
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 266 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 296
>pdb|1LWC|A Chain A, Crystal Structure Of M184v Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYVDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|2HNY|A Chain A, Crystal Structure Of E138k Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|2HNZ|A Chain A, Crystal Structure Of E138k Mutant Hiv-1 Reverse
Transcriptase In Complex With Pett-2
Length = 534
Score = 40.8 bits (94), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 53/217 (24%), Positives = 89/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYN----GDVLAMTCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N G LP G +
Sbjct: 94 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNKTPGIRYQYNVLPQGWKGS 153
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 154 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 212
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 213 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 260
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 261 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 291
>pdb|3DMJ|A Chain A, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse
Transcriptase In Complex With Gw564511
Length = 560
Score = 40.8 bits (94), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 89/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSATVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVICQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|1HVU|B Chain B, Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Complexed With A 33-Base Nucleotide Rna Pseudoknot
pdb|1HVU|E Chain E, Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Complexed With A 33-Base Nucleotide Rna Pseudoknot
pdb|1HVU|H Chain H, Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Complexed With A 33-Base Nucleotide Rna Pseudoknot
pdb|1HVU|K Chain K, Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Complexed With A 33-Base Nucleotide Rna Pseudoknot
Length = 423
Score = 40.8 bits (94), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 60/276 (21%), Positives = 117/276 (42%), Gaps = 32/276 (11%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLIN-HFRIP 539
EM + G + ++ + + +F + K + R +++ + LN+ + F + P
Sbjct: 36 EMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNK--RTQDFWEVQLGIPHP 93
Query: 540 SFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAP 592
+ L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 94 AGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSP 153
Query: 593 QAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL 650
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 154 AIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTT 212
Query: 651 QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYL 710
P FL + ++ H D+ T+ I+ L +W ++ + L+G L
Sbjct: 213 PDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKL 260
Query: 711 SFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
++AS + P ++++ LLR G LT + P
Sbjct: 261 NWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 290
>pdb|1IKV|A Chain A, K103n Mutant Hiv-1 Reverse Transcriptase In Complex With
Efivarenz
pdb|1IKX|A Chain A, K103n Mutant Hiv-1 Reverse Transcriptase In Complex With
The Inhibitor Pnu142721
pdb|1IKY|A Chain A, Hiv-1 Reverse Transcriptase In Complex With The Inhibitor
Msc194
Length = 560
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1LWE|A Chain A, Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse
Transcriptase (Rtmn) In Complex With Nevirapine
Length = 560
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLY 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|4DG1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Polymorphism Mutation K172a And K173a
Length = 549
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + ++ +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFAAQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1LW0|A Chain A, Crystal Structure Of T215y Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1LW2|A Chain A, Crystal Structure Of T215y Mutant Hiv-1 Reverse
Transcriptase In Complex With 1051u91
Length = 560
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLY 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|1S1W|A Chain A, Crystal Structure Of V106a Mutant Hiv-1 Reverse
Transcriptase In Complex With Uc-781
Length = 560
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 89/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSATVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|2OPQ|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw420867x
Length = 534
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ ++K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 94 PAGIKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 153
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 154 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 212
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 213 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 260
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 261 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 291
>pdb|3QLH|A Chain A, Hiv-1 Reverse Transcriptase In Complex With Manicol At The
Rnase H Active Site And Tmc278 (rilpivirine) At The
Nnrti Binding Pocket
Length = 555
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 98 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 157
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + ++ +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 PAIFQSSMTKILEPFAAQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 216
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 217 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 264
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 265 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 295
>pdb|1S1T|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Uc-781
pdb|1S1U|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
pdb|1S1V|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Tnk-651
pdb|3DOL|A Chain A, Crystal Structure Of L100i Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw695634
Length = 560
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ ++K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGIKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|1EET|A Chain A, Hiv-1 Reverse Transcriptase In Complex With The Inhibitor
Msc204
Length = 557
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2ZD1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Tmc278 (Rilpivirine), A Non-Nucleoside Rt
Inhibitor
pdb|4H4M|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With (E)-
3-(3-Chloro-5-(4-Chloro-2-(2-(2,4-Dioxo-3,4-
Dihydropyrimidin-1(2h)-
Yl)ethoxy)phenoxy)phenyl)acrylonitrile (Jlj494), A
Non-Nucleoside Inhibitor
pdb|4H4O|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With
(E)-3-(3-(2-(2-(2,4-Dioxo-3,
4-Dihydropyrimidin-1(2h)-Yl)ethoxy)- 4-
Fluorophenoxy)-5-Fluorophenyl)acrylonitrile (Jlj506), A
Non- Nucleoside Inhibitor
pdb|4I2P|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Rilpivirine (tmc278) Based Analogue
pdb|4G1Q|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (rt) In
Complex With Rilpivirine (tmc278, Edurant), A
Non-nucleoside Rt-inhibiting Drug
pdb|4I7G|A Chain A, Hiv-1 Reverse Transcriptase With Bound Fragment At Nnrti
Adjacent Site
pdb|4ICL|A Chain A, Hiv-1 Reverse Transcriptase With Bound Fragment At The
Incoming Dntp Binding Site
pdb|4ID5|A Chain A, Hiv-1 Reverse Transcriptase With Bound Fragment At The
Rnase H Primer Grip Site
pdb|4IDK|A Chain A, Hiv-1 Reverse Transcriptase With Bound Fragment At The 428
Site
pdb|4IFV|A Chain A, Detecting Allosteric Sites Of Hiv-1 Reverse Transcriptase
By X-ray Crystallographic Fragment Screening
pdb|4IFY|A Chain A, Hiv-1 Reverse Transcriptase With Bound Fragment At The
Knuckles Site
pdb|4IG0|A Chain A, Hiv-1 Reverse Transcriptase With Bound Fragment At The 507
Site
pdb|4IG3|A Chain A, Hiv-1 Reverse Transcriptase With Bound Fragment Near
Knuckles Site
Length = 557
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 99 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 158
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + ++ +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 PAIFQSSMTKILEPFAAQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 217
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 218 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 265
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 266 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 296
>pdb|3IRX|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With The Non-Nucleoside Rt Inhibitor
(E)-S-Methyl
5-(1-(3,7-Dimethyl-2-Oxo-2,
3-Dihydrobenzo[d]oxazol-5-Yl)-5-
(5-Methyl-1,3,4-Oxadiazol-2-Yl)pent-1-Enyl)-2-Methoxy-3-
Methylbenzothioate.
pdb|3IS9|A Chain A, Crystal Structure Of The Hiv-1 Reverse Transcriptase (Rt)
In Complex With The Alkenyldiarylmethane (Adam)
Non-Nucleoside Rt Inhibitor Dimethyl
3,3'-(6-Methoxy-6-Oxohex-1-Ene-1,1-
Diyl)bis(5-Cyano-6-Methoxybenzoate)
Length = 558
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 100 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 159
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + ++ +V+ Y+DD L V D I + + K+ L W +
Sbjct: 160 PAIFQSSMTKILEPFAAQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 218
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 219 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 266
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 267 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 297
>pdb|3HVT|A Chain A, Structural Basis Of Asymmetry In The Human
Immunodeficiency Virus Type 1 Reverse Transcriptase
Heterodimer
Length = 556
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2VG5|A Chain A, Crystal Structures Of Hiv-1 Reverse Transcriptase
Complexes With Thiocarbamate Non-Nucleoside Inhibitors
pdb|2VG6|A Chain A, Crystal Structures Of Hiv-1 Reverse Transcriptase
Complexes With Thiocarbamate Non-Nucleoside Inhibitors
pdb|2VG7|A Chain A, Crystal Structures Of Hiv-1 Reverse Transcriptase
Complexes With Thiocarbamate Non-Nucleoside Inhibitors
Length = 557
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|3JSM|A Chain A, K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To
Ds-Dna And Complexed With Tenofovir-Diphosphate As The
Incoming Nucleotide Substrate
pdb|3JYT|A Chain A, K65r Mutant Hiv-1 Reverse Transcriptase Cross-Linked To
Ds- Dna And Complexed With Datp As The Incoming
Nucleotide Substrate
Length = 558
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDICKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1N5Y|A Chain A, Hiv-1 Reverse Transcriptase Crosslinked To Post-
Translocation Aztmp-Terminated Dna (Complex P)
pdb|1N6Q|A Chain A, Hiv-1 Reverse Transcriptase Crosslinked To Pre-
Translocation Aztmp-Terminated Dna (Complex N)
pdb|1T03|A Chain A, Hiv-1 Reverse Transcriptase Crosslinked To Tenofovir
Terminated Template-Primer (Complex P)
pdb|1T05|A Chain A, Hiv-1 Reverse Transcriptase Crosslinked To Template-Primer
With Tenofovir-Diphosphate Bound As The Incoming
Nucleotide Substrate
pdb|1R0A|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase
Covalently Tethered To Dna Template-primer Solved To 2.8
Angstroms
Length = 558
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDICKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|1HMV|A Chain A, The Structure Of Unliganded Reverse Transcriptase From The
Human Immunodeficiency Virus Type 1
pdb|1TV6|A Chain A, Hiv-1 Reverse Transcriptase Complexed With Cp-94,707
pdb|1HMV|C Chain C, The Structure Of Unliganded Reverse Transcriptase From The
Human Immunodeficiency Virus Type 1
pdb|1HMV|E Chain E, The Structure Of Unliganded Reverse Transcriptase From The
Human Immunodeficiency Virus Type 1
pdb|1HMV|G Chain G, The Structure Of Unliganded Reverse Transcriptase From The
Human Immunodeficiency Virus Type 1
Length = 560
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1HVU|A Chain A, Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Complexed With A 33-Base Nucleotide Rna Pseudoknot
pdb|1HVU|D Chain D, Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Complexed With A 33-Base Nucleotide Rna Pseudoknot
pdb|1HVU|G Chain G, Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Complexed With A 33-Base Nucleotide Rna Pseudoknot
pdb|1HVU|J Chain J, Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Complexed With A 33-Base Nucleotide Rna Pseudoknot
Length = 554
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|1LWF|A Chain A, Crystal Structure Of A Mutant Hiv-1 Reverse Transcriptase
(rtmq+m184v: M41l/d67n/k70r/m184v/t215y) In Complex With
Nevirapine
Length = 560
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYVDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLY 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLXKLLRGTKALTEVIP 294
>pdb|1IKW|A Chain A, Wild Type Hiv-1 Reverse Transcriptase In Complex With
Efavirenz
pdb|3ISN|C Chain C, Crystal Structure Of Hiv-1 Rt Bound To A 6-Vinylpyrimidine
Inhibitor
pdb|3ITH|A Chain A, Crystal Structure Of The Hiv-1 Reverse Transcriptase Bound
To A 6-Vinylpyrimidine Inhibitor
pdb|3ITH|C Chain C, Crystal Structure Of The Hiv-1 Reverse Transcriptase Bound
To A 6-Vinylpyrimidine Inhibitor
Length = 560
Score = 40.0 bits (92), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 92/217 (42%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|2YKM|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With A Difluoromethylbenzoxazole (Dfmb)
Pyrimidine Thioether Derivative, A Non-Nucleoside Rt
Inhibitor (Nnrti)
Length = 562
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 58/275 (21%), Positives = 117/275 (42%), Gaps = 30/275 (10%)
Query: 482 EMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSLINHFRIPS 540
EM + G + ++ + + +F + K + R +++ + LN+ + + + P+
Sbjct: 40 EMEKEGKISKIGPENPYSTPVFAIKKKDSTKWRKLVDFRELNK-RTQDFWEVQLGIPHPA 98
Query: 541 FLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATAPQ 593
L+K + +D+ AYF VP+ +++ A S N + + LP G +P
Sbjct: 99 GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPA 158
Query: 594 AFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQ 651
F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 IFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLTTP 217
Query: 652 KSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGYLS 711
P ++G ++ H D+ T+ I+ L +W ++ + L+G L+
Sbjct: 218 DKKHQKEPPCLWMG--YELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGKLN 265
Query: 712 FASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
+AS + P ++++ LLR G LT + P
Sbjct: 266 WASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|3V4I|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Dna And Azttp
pdb|3V4I|C Chain C, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Dna And Azttp
pdb|3V6D|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt)
Cross-Linked With Azt-Terminated Dna
pdb|3V6D|C Chain C, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt)
Cross-Linked With Azt-Terminated Dna
pdb|3V81|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Dna And The Nonnucleoside Inhibitor Nevirapine
pdb|3V81|C Chain C, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Dna And The Nonnucleoside Inhibitor Nevirapine
Length = 556
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 99 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 158
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 217
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ L+G
Sbjct: 218 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDICKLVGK 265
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 266 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 296
>pdb|3KLF|A Chain A, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|E Chain E, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|I Chain I, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
pdb|3KLF|M Chain M, Crystal Structure Of Wild-Type Hiv-1 Reverse Transcriptase
Crosslinked To A Dsdna With A Bound Excision Product,
Aztppppa
Length = 557
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 99 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 158
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 217
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ L+G
Sbjct: 218 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDICKLVGK 265
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 266 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 296
>pdb|2ZE2|A Chain A, Crystal Structure Of L100iK103N MUTANT HIV-1 Reverse
Transcriptase (Rt) In Complex With Tmc278 (Rilpivirine),
A Non-Nucleoside Rt Inhibitor
Length = 557
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ ++K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 99 PAGIKKNKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 158
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + ++ +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 PAIFQSSMTKILEPFAAQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 217
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 218 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 265
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 266 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 296
>pdb|1RTD|A Chain A, Structure Of A Catalytic Complex Of Hiv-1 Reverse
Transcriptase: Implications For Nucleoside Analog Drug
Resistance
pdb|1RTD|C Chain C, Structure Of A Catalytic Complex Of Hiv-1 Reverse
Transcriptase: Implications For Nucleoside Analog Drug
Resistance
Length = 554
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 52/217 (23%), Positives = 91/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + R + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAIFQSSMTKILEPFRKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDICKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++++ LLR G LT + P
Sbjct: 264 LNWASQIYP-----GIKVRQLCKLLR-GTKALTEVIP 294
>pdb|3KLE|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To A Dsdna With A Bound
Excision Product, Aztppppa
pdb|3KLE|E Chain E, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To A Dsdna With A Bound
Excision Product, Aztppppa
pdb|3KLE|I Chain I, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To A Dsdna With A Bound
Excision Product, Aztppppa
pdb|3KLE|M Chain M, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To A Dsdna With A Bound
Excision Product, Aztppppa
pdb|3KLG|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To Pre-Translocation
Aztmp-Terminated Dna (Complex N)
pdb|3KLG|E Chain E, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To Pre-Translocation
Aztmp-Terminated Dna (Complex N)
pdb|3KLI|A Chain A, Crystal Structure Of Unliganded Azt-Resistant Hiv-1
Reverse Transcriptase
Length = 562
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 54/219 (24%), Positives = 92/219 (42%), Gaps = 32/219 (14%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 99 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 158
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLY 217
Query: 650 L--QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLL 707
QK P FL + ++ H D+ T+ I+ L +W ++ L+
Sbjct: 218 TPDQKHQKEPP----FLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDICKLV 263
Query: 708 GYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
G L++AS + P ++ RQ S L G LT + P
Sbjct: 264 GKLNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 296
>pdb|3KLH|A Chain A, Crystal Structure Of Azt-Resistant Hiv-1 Reverse
Transcriptase Crosslinked To Post-Translocation
Aztmp-Terminated Dna (Complex P)
Length = 564
Score = 39.7 bits (91), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 54/219 (24%), Positives = 92/219 (42%), Gaps = 32/219 (14%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 99 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 158
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P F S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 PAIFQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLY 217
Query: 650 L--QKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLL 707
QK P FL + ++ H D+ T+ I+ L +W ++ L+
Sbjct: 218 TPDQKHQKEPP----FLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDICKLV 263
Query: 708 GYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
G L++AS + P ++ RQ S L G LT + P
Sbjct: 264 GKLNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 296
>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta-
Thujaplicinol Bound At The Rnase H Active Site
Length = 555
Score = 38.1 bits (87), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 97 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 156
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 157 PAISQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 215
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 216 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 263
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 264 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 294
>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1
Reverse Transcriptase, Rt69a
Length = 556
Score = 38.1 bits (87), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 98 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 157
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 158 PAISQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 216
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 217 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 264
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 265 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 295
>pdb|3QO9|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Tsao-T, A Non-Nucleoside Rt Inhibitor
(Nnrti)
Length = 557
Score = 38.1 bits (87), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 51/217 (23%), Positives = 90/217 (41%), Gaps = 28/217 (12%)
Query: 539 PSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYNGDVLAM----TCLPFGLATA 591
P+ L+K + +D+ AYF VP+ +++ A S N + + LP G +
Sbjct: 99 PAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGS 158
Query: 592 PQAFASLSNWVASLLRSRGMRVVV--YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVN 649
P S + + + +V+ Y+DD L V D I + + K+ L W +
Sbjct: 159 PAISQSSMTKILEPFKKQNPDIVIYQYMDD-LYVGSDLEIGQHRTKIEELRQHLLRWGLT 217
Query: 650 LQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDKQLTLGNILRTLLASKTWNLDSARSLLGY 709
P FL + ++ H D+ T+ I+ L +W ++ + L+G
Sbjct: 218 TPDKKHQKEP--PFLWMGYELHPDKW--------TVQPIV--LPEKDSWTVNDIQKLVGK 265
Query: 710 LSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINP 746
L++AS + P ++ RQ S L G LT + P
Sbjct: 266 LNWASQIYPGIKV------RQLSKLLRGTKALTEVIP 296
>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 555
Score = 33.9 bits (76), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 54/265 (20%), Positives = 105/265 (39%), Gaps = 44/265 (16%)
Query: 474 SAMSLHIQEMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSL 532
A+ ++M + G L+ T + + F + K + R +++ + LN+ + F+
Sbjct: 32 EALKEICEKMEKEGQLEEAPPTNPYNTPTFAIKKKDKNKWRMLIDFRELNKVT--QDFTE 89
Query: 533 IN-HFRIPSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYN----GDVLAMTCL 584
I P+ L K + +D+ AYF +P+ + + A S N G L
Sbjct: 90 IQLGIPHPAGLAKKRRITVLDVGDAYFSIPLHEDFRPYTAFTLPSVNNAEPGKRYIYKVL 149
Query: 585 PFGLATAPQAFASLSNWVASLLRSRGMRVVV--YLDDFLL------VNQDPRILEIQGKL 636
P G +P F V R V++ Y+DD L+ + D +L+++
Sbjct: 150 PQGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDRTDLEHDRVVLQLK--- 206
Query: 637 AVSILGSLGWIVNLQKSSLSPAPVLQFLGIMWDP---HLDRMWLPEDKQLTLGNILRTLL 693
+L LG+ +K P ++G P L ++ LP+
Sbjct: 207 --ELLNGLGFSTPDEK--FQKDPPYHWMGYELWPTKWKLQKIQLPQ-------------- 248
Query: 694 ASKTWNLDSARSLLGYLSFASFVIP 718
+ W ++ + L+G L++A+ + P
Sbjct: 249 -KEIWTVNDIQKLVGVLNWAAQLYP 272
>pdb|1MU2|B Chain B, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 426
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 53/265 (20%), Positives = 103/265 (38%), Gaps = 44/265 (16%)
Query: 474 SAMSLHIQEMLETGVLKRLDSTTGFLSRLFLVPKGNGGT-RPVLNLKGLNQFLSPKKFSL 532
A+ ++M + G L+ T + + F + K + R +++ + LN+ + F+
Sbjct: 27 EALKEICEKMEKEGQLEEAPPTNPYNTPTFAIKKKDKNKWRMLIDFRELNKVT--QDFTE 84
Query: 533 IN-HFRIPSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLAL---SYN----GDVLAMTCL 584
I P+ L K + +D+ AYF +P+ + + A S N G L
Sbjct: 85 IQLGIPHPAGLAKKRRITVLDVGDAYFSIPLHEDFRPYTAFTLPSVNNAEPGKRYIYKVL 144
Query: 585 PFGLATAPQAFASLSNWVASLLRSRGMRVVV--YLDDFLL------VNQDPRILEIQGKL 636
P G +P F V R V++ Y+DD L+ + D +L+++
Sbjct: 145 PQGWKGSPAIFQHTMRQVLEPFRKANKDVIIIQYMDDILIASDRTDLEHDRVVLQLK--- 201
Query: 637 AVSILGSLGWIVNLQKSSLSPAPVLQFLGIMWDP---HLDRMWLPEDKQLTLGNILRTLL 693
+L LG + P ++G P L ++ LP+
Sbjct: 202 --ELLNGLG--FSTPDEKFQKDPPYHWMGYELWPTKWKLQKIQLPQ-------------- 243
Query: 694 ASKTWNLDSARSLLGYLSFASFVIP 718
+ W ++ + L+G L++A+ + P
Sbjct: 244 -KEIWTVNDIQKLVGVLNWAAQLYP 267
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.133 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,245,047
Number of Sequences: 62578
Number of extensions: 1108997
Number of successful extensions: 2668
Number of sequences better than 100.0: 131
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 131
Number of HSP's that attempted gapping in prelim test: 2555
Number of HSP's gapped (non-prelim): 131
length of query: 1097
length of database: 14,973,337
effective HSP length: 109
effective length of query: 988
effective length of database: 8,152,335
effective search space: 8054506980
effective search space used: 8054506980
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)