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= psy2243
(405 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GMH|A Chain A, Structure Of Porcine Electron Transfer Flavoprotein-
Ubiquinone Oxidoreductase In Complexed With Ubiquinone
pdb|2GMH|B Chain B, Structure Of Porcine Electron Transfer Flavoprotein-
Ubiquinone Oxidoreductase In Complexed With Ubiquinone
pdb|2GMJ|A Chain A, Structure Of Porcine Electron Transfer Flavoprotein-
Ubiquinone Oxidoreductase
pdb|2GMJ|B Chain B, Structure Of Porcine Electron Transfer Flavoprotein-
Ubiquinone Oxidoreductase
Length = 584
Score = 135 bits (340), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 66/96 (68%), Positives = 74/96 (77%)
Query: 278 GIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEG 337
GI G+ T K + D+ LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE
Sbjct: 439 GIFYWIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEH 498
Query: 338 DQPAHLTLKDDSVPVNTNLAVYDGPEGRFCPAGKLE 373
DQPAHLTLKDDSVPVN NL++YDGPE RFCPAG E
Sbjct: 499 DQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYE 534
>pdb|2QK9|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 18-Mer RnaDNA HYBRID
pdb|2QKK|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|E Chain E, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|F Chain F, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|I Chain I, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|J Chain J, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|M Chain M, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|N Chain N, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|R Chain R, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|S Chain S, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|W Chain W, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
Length = 154
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 57/144 (39%), Gaps = 19/144 (13%)
Query: 144 GDFVQVYTDGSKSDSS-----VGCAFVIPQLHIVKKQTLNP-KSSIFHAELLAISDAVST 197
GDFV VYTDG S + G H + P + + AE+ A A+
Sbjct: 5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQ 64
Query: 198 IKSQSIGEAVIISDSLSALQAISSMSHS---NPLVQSIHEEI----------STIPNSTI 244
K+Q+I + V+ ++S+ + I++ N S +E+ I
Sbjct: 65 AKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDI 124
Query: 245 KFFWCPSHVGIAGNDAADLEAKSA 268
++ P H G GN+ AD A+
Sbjct: 125 QWMHVPGHSGFIGNEEADRLAREG 148
>pdb|1O1W|A Chain A, Solution Structure Of The Rnase H Domain Of The Hiv-1
Reverse Transcriptase In The Presence Of Magnesium
Length = 138
Score = 34.7 bits (78), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 70 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 127
>pdb|3K2P|A Chain A, Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain With
The Inhibitor Beta-Thujaplicinol Bound At The Active
Site
pdb|3K2P|B Chain B, Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain With
The Inhibitor Beta-Thujaplicinol Bound At The Active
Site
Length = 136
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 68 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 125
>pdb|1HRH|A Chain A, Crystal Structure Of The Ribonuclease H Domain Of Hiv-1
Reverse Transcriptase
pdb|1HRH|B Chain B, Crystal Structure Of The Ribonuclease H Domain Of Hiv-1
Reverse Transcriptase
Length = 136
Score = 34.7 bits (78), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 66 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 123
>pdb|3LP3|A Chain A, P15 Hiv Rnaseh Domain With Inhibitor Mk3
pdb|3LP3|B Chain B, P15 Hiv Rnaseh Domain With Inhibitor Mk3
Length = 138
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 68 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 125
>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 = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1RT3|A Chain A, Azt Drug Resistant Hiv-1 Reverse Transcriptase Complexed
With 1051u91
Length = 560
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|2I5J|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Dhbnh, An Rnase H Inhibitor
Length = 552
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1S1W|A Chain A, Crystal Structure Of V106a Mutant Hiv-1 Reverse
Transcriptase In Complex With Uc-781
Length = 560
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1LWE|A Chain A, Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse
Transcriptase (Rtmn) In Complex With Nevirapine
Length = 560
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1S1X|A Chain A, Crystal Structure Of V108i Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 495 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 552
>pdb|1LWC|A Chain A, Crystal Structure Of M184v Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 205 EAVIISDS---LSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAA 261
E I++DS L +QA S S LV I E++ I + W P+H GI GN+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESE-LVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQV 548
Query: 262 D 262
D
Sbjct: 549 D 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1HYS|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With A Polypurine Tract Rna:dna
Length = 553
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 205 EAVIISDS---LSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAA 261
E I++DS L +QA S S LV I E++ I + W P+H GI GN+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESE-LVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQV 548
Query: 262 D 262
D
Sbjct: 549 D 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1EET|A Chain A, Hiv-1 Reverse Transcriptase In Complex With The Inhibitor
Msc204
Length = 557
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|3DMJ|A Chain A, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse
Transcriptase In Complex With Gw564511
Length = 560
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 205 EAVIISDS---LSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAA 261
E I++DS L +QA S S LV I E++ I + W P+H GI GN+
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESE-LVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQV 548
Query: 262 D 262
D
Sbjct: 549 D 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDESESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1
Reverse Transcriptase, Rt69a
Length = 556
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 493 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 550
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1UWB|A Chain A, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo
Length = 558
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1JLF|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|3FFI|A Chain A, Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor
Length = 561
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 493 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 550
>pdb|1DLO|A Chain A, Human Immunodeficiency Virus Type 1
pdb|1BQM|A Chain A, Hiv-1 RtHBY 097
Length = 556
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 35/120 (29%), Positives = 53/120 (44%), Gaps = 18/120 (15%)
Query: 150 YTDGSKS-DSSVGCAFVIP----QLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 204
Y DG+ S ++ +G A + Q + T N K+ + A LA+ D S
Sbjct: 441 YVDGAASRETKLGKAGYVTNKGRQKVVTLTDTTNQKTEL-QAIHLALQD--------SGL 491
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|4DG1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Polymorphism Mutation K172a And K173a
Length = 549
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1JXB|A Chain A, I53a, A Point Mutant Of The Cysteine-Free Variant Of E.
Coli Rnase Hi
Length = 155
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 33/148 (22%), Positives = 63/148 (42%), Gaps = 18/148 (12%)
Query: 147 VQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNP---KSSIFHAELLAISDAVSTIKSQSI 203
V+++TDGS + + + +++T + +++ EL+A + A+ +K +
Sbjct: 5 VEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAAVALEALKEHA- 63
Query: 204 GEAVIISDSLSALQAISSMSHS-----------NPL--VQSIHEEISTIPNSTIKFFWCP 250
E ++ +DS Q I+ H+ P+ V + + IK+ W
Sbjct: 64 -EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVK 122
Query: 251 SHVGIAGNDAADLEAKSALENPISHDHG 278
H G N+ AD A++A NP D G
Sbjct: 123 GHAGHPENERADELARAAAMNPTLEDTG 150
>pdb|2YNF|A Chain A, Hiv-1 Reverse Transcriptase Y188l Mutant In Complex With
Inhibitor Gsk560
Length = 563
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 205 EAVIISDS---LSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAA 261
E I++DS L +QA S S LV I E++ I + W P+H GI GN+
Sbjct: 495 EVNIVTDSQYALGIIQAQPDQSESE-LVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQV 551
Query: 262 D 262
D
Sbjct: 552 D 552
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta-
Thujaplicinol Bound At The Rnase H Active Site
Length = 555
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 495 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 552
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|3DRR|A Chain A, Hiv Reverse Transcriptase Y181c Mutant In Complex With
Inhibitor R8e
Length = 563
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 495 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 552
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|3HVT|A Chain A, Structural Basis Of Asymmetry In The Human
Immunodeficiency Virus Type 1 Reverse Transcriptase
Heterodimer
Length = 556
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1RDH|A Chain A, Crystallographic Analyses Of An Active Hiv-1 Ribonuclease
H Domain Show Structural Features That Distinguish It
From The Inactive Form
pdb|1RDH|B Chain B, Crystallographic Analyses Of An Active Hiv-1 Ribonuclease
H Domain Show Structural Features That Distinguish It
From The Inactive Form
Length = 146
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 78 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 135
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 495 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 552
>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 = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 493 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 550
>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 = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>pdb|2QKB|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 20-Mer RnaDNA HYBRID
pdb|2QKB|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 20-Mer RnaDNA HYBRID
Length = 154
Score = 33.5 bits (75), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 35/144 (24%), Positives = 56/144 (38%), Gaps = 19/144 (13%)
Query: 144 GDFVQVYTDGSKSDSS-----VGCAFVIPQLHIVKKQTLNP-KSSIFHAELLAISDAVST 197
GDFV VYTDG S + G H + P + + AE+ A A+
Sbjct: 5 GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQ 64
Query: 198 IKSQSIGEAVIISDSLSALQAISSMSHS---NPLVQSIHEEI----------STIPNSTI 244
K+Q+I + V+ ++S + I++ N S +E+ I
Sbjct: 65 AKTQNINKLVLYTNSXFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGXDI 124
Query: 245 KFFWCPSHVGIAGNDAADLEAKSA 268
++ P H G GN+ AD A+
Sbjct: 125 QWXHVPGHSGFIGNEEADRLAREG 148
>pdb|1BQN|A Chain A, Tyr 188 Leu Hiv-1 RtHBY 097
Length = 558
Score = 33.1 bits (74), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN D
Sbjct: 492 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNQQVD 549
>pdb|1F21|A Chain A, Divalent Metal Cofactor Binding In The Kinetic Folding
Trajectory Of E. Coli Ribonuclease Hi
Length = 155
Score = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 33/148 (22%), Positives = 62/148 (41%), Gaps = 18/148 (12%)
Query: 147 VQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNP---KSSIFHAELLAISDAVSTIKSQSI 203
V+++TDGS + + + +++T + +++ EL+A A+ +K +
Sbjct: 5 VEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHA- 63
Query: 204 GEAVIISDSLSALQAISSMSHS-----------NPL--VQSIHEEISTIPNSTIKFFWCP 250
E ++ +DS Q I+ H+ P+ V + + IK+ W
Sbjct: 64 -EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVK 122
Query: 251 SHVGIAGNDAADLEAKSALENPISHDHG 278
H G N+ AD A++A NP D G
Sbjct: 123 GHAGHPENERADELARAAAMNPTLEDTG 150
>pdb|1G15|A Chain A, Co-Crystal Of E. Coli Rnase Hi With Two Mn2+ Ions Bound In
The The Active Site
Length = 155
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 33/148 (22%), Positives = 62/148 (41%), Gaps = 18/148 (12%)
Query: 147 VQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNP---KSSIFHAELLAISDAVSTIKSQSI 203
V+++TDGS + + + +++T + +++ EL+A A+ +K +
Sbjct: 5 VEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHA- 63
Query: 204 GEAVIISDSLSALQAISSMSHS-----------NPL--VQSIHEEISTIPNSTIKFFWCP 250
E ++ +DS Q I+ H+ P+ V + + IK+ W
Sbjct: 64 -EVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVK 122
Query: 251 SHVGIAGNDAADLEAKSALENPISHDHG 278
H G N+ AD A++A NP D G
Sbjct: 123 GHAGHPENERADELARAAAMNPTLEDTG 150
>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 555
Score = 32.0 bits (71), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 51/116 (43%), Gaps = 10/116 (8%)
Query: 150 YTDGS-KSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVI 208
YTDGS S G A + K + L +++ AEL A + A++ S + I
Sbjct: 440 YTDGSCNRQSKEGKAGYVTDRGKDKVKKLE-QTTNQQAELEAFAMALT----DSGPKVNI 494
Query: 209 ISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
I DS + ++S + +V I EE+ I I W P+H GI GN D
Sbjct: 495 IVDSQYVMGIVASQPTESESKIVNQIIEEM--IKKEAIYVAWVPAHKGIGGNQEVD 548
>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 = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 212 SLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
+L +QA S S LV I E++ I + W P+H GI GN+ D
Sbjct: 502 ALGIIQAQPDQSESE-LVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 32.0 bits (71), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 212 SLSALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
+L +QA S S LV I E++ I + W P+H GI GN+ D
Sbjct: 502 ALGIIQAQPDQSESE-LVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 549
>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 = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I+++S AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTNSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>pdb|2OPR|A Chain A, Crystal Structure Of K101e Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw420867x
Length = 547
Score = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGND 259
E I++DS AL I + + LV I E++ I + W P+H GI GN+
Sbjct: 491 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNE 545
>pdb|3AA2|A Chain A, A52i E. Coli Rnase Hi
Length = 155
Score = 31.6 bits (70), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 42/105 (40%), Gaps = 15/105 (14%)
Query: 187 ELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHS-----------NPL--VQSIH 233
EL+AI A+ +K E ++ +DS Q I+ H+ P+ V
Sbjct: 48 ELMAIIVALEALKEHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQ 105
Query: 234 EEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHG 278
+ + IK+ W H G N+ D A++A NP D G
Sbjct: 106 RLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTG 150
>pdb|1JL1|A Chain A, D10a E. Coli Ribonuclease Hi
Length = 155
Score = 31.2 bits (69), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 43/105 (40%), Gaps = 15/105 (14%)
Query: 187 ELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHS-----------NPL--VQSIH 233
EL+A A+ +K + E ++ +DS Q I+ H+ P+ V
Sbjct: 48 ELMAAIVALEALKEHA--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQ 105
Query: 234 EEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHG 278
+ + IK+ W H G N+ AD A++A NP D G
Sbjct: 106 RLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTG 150
>pdb|3AA4|A Chain A, A52v E.Coli Rnase Hi
Length = 155
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 15/105 (14%)
Query: 187 ELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHS-----------NPL--VQSIH 233
EL+A+ A+ +K E ++ +DS Q I+ H+ P+ V
Sbjct: 48 ELMAVIVALEALKEHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQ 105
Query: 234 EEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHG 278
+ + IK+ W H G N+ D A++A NP D G
Sbjct: 106 RLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTG 150
>pdb|2OPP|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw420867x
Length = 542
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGN 258
E I++DS AL I + + LV I E++ I + W P+H GI GN
Sbjct: 489 EVNIVTDSQYALGIIQAQPDQSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGN 542
>pdb|3AA3|A Chain A, A52l E. Coli Rnase Hi
Length = 155
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 32/148 (21%), Positives = 61/148 (41%), Gaps = 18/148 (12%)
Query: 147 VQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNP---KSSIFHAELLAISDAVSTIKSQSI 203
V+++TDGS + + + +++T + +++ EL+A+ A+ +K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMALIVALEALKEHC- 63
Query: 204 GEAVIISDSLSALQAISSMSHS-----------NPL--VQSIHEEISTIPNSTIKFFWCP 250
E ++ +DS Q I+ H+ P+ V + + IK+ W
Sbjct: 64 -EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVK 122
Query: 251 SHVGIAGNDAADLEAKSALENPISHDHG 278
H G N+ D A++A NP D G
Sbjct: 123 GHAGHPENERCDELARAAAMNPTLEDTG 150
>pdb|1GOB|A Chain A, Cooperative Stabilization Of Escherichia Coli Ribonuclease
Hi By Insertion Of Gly-80b And Gly-77-> Ala Substitution
Length = 155
Score = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 42/105 (40%), Gaps = 15/105 (14%)
Query: 187 ELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHS-----------NPL--VQSIH 233
EL+A A+ +K E ++ +DS QAI+ H+ P+ V
Sbjct: 48 ELMAAIVALEALKEHC--EVILSTDSQYVRQAITQWIHNWKKRGWKTADKKPVKNVDLWQ 105
Query: 234 EEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHG 278
+ + IK+ W H G N+ D A++A NP D G
Sbjct: 106 RLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAMNPTLEDTG 150
>pdb|3AA5|X Chain X, A52f E.Coli Rnase Hi
Length = 155
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 32/148 (21%), Positives = 60/148 (40%), Gaps = 18/148 (12%)
Query: 147 VQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNP---KSSIFHAELLAISDAVSTIKSQSI 203
V+++TDGS + + + +++T + +++ EL+A A+ +K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAFIVALEALKEHC- 63
Query: 204 GEAVIISDSLSALQAISSMSHS-----------NPL--VQSIHEEISTIPNSTIKFFWCP 250
E ++ +DS Q I+ H+ P+ V + + IK+ W
Sbjct: 64 -EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVK 122
Query: 251 SHVGIAGNDAADLEAKSALENPISHDHG 278
H G N+ D A++A NP D G
Sbjct: 123 GHAGHPENERCDELARAAAMNPTLEDTG 150
>pdb|1RBU|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 32/148 (21%), Positives = 62/148 (41%), Gaps = 18/148 (12%)
Query: 147 VQVYTDGSKSDSSVGCAFVIPQLHIVKKQTLNP---KSSIFHAELLAISDAVSTIKSQSI 203
V+++TDGS + + + +++T + +++ EL+A A+ +K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHC- 63
Query: 204 GEAVIISDSLSALQAISSMSHS----------NPLVQSI---HEEISTIPNSTIKFFWCP 250
E ++ +DS Q I+ H+ N V+++ + + IK+ W
Sbjct: 64 -EVILSTDSQYVRQGITQWIHNWKKRGWKTADNKPVKNVDLWQRLDAALGQHQIKWEWVK 122
Query: 251 SHVGIAGNDAADLEAKSALENPISHDHG 278
H G N+ D A++A NP D G
Sbjct: 123 GHAGHPENERCDELARAAAMNPTLEDTG 150
>pdb|3MIS|A Chain A, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-8g)
pdb|3MIS|B Chain B, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
(-8g)
Length = 161
Score = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 102 EPKESWLHKKPSCNLSLT-LYKKDGMPH--QVFQQEFQR-NMNENYGDFVQVYTDGSKSD 157
EP+ + K L+++ + +KD P+ ++ Q +R N+ ++ GD + YT +
Sbjct: 25 EPRPDYKDIKYQVRLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIYGSTH 84
Query: 158 SSVGCAFVIPQLHIVKKQT 176
S+ ++P L I KKQ
Sbjct: 85 LSIILPDLVPYLRIKKKQA 103
>pdb|3HZZ|A Chain A, 2.4 Angstrom Crystal Structure Of Streptomyces Collinus
Crotonyl Coa CarboxylaseREDUCTASE
pdb|3HZZ|B Chain B, 2.4 Angstrom Crystal Structure Of Streptomyces Collinus
Crotonyl Coa CarboxylaseREDUCTASE
pdb|3HZZ|C Chain C, 2.4 Angstrom Crystal Structure Of Streptomyces Collinus
Crotonyl Coa CarboxylaseREDUCTASE
pdb|3HZZ|D Chain D, 2.4 Angstrom Crystal Structure Of Streptomyces Collinus
Crotonyl Coa CarboxylaseREDUCTASE
Length = 467
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 294 PQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSVPVN 353
P D+T L P E +F L+ +AL TN +P HLT ++ + P
Sbjct: 175 PDGHDDTMLDPEQRIWGFE-------TNFGGLAEIALVKTNQLMPKPKHLTWEEAAAPGL 227
Query: 354 TNLAVY 359
N Y
Sbjct: 228 VNSTAY 233
>pdb|1RYL|A Chain A, The Crystal Structure Of A Protein Of Unknown Function
Yfbm From Escherichia Coli
pdb|1RYL|B Chain B, The Crystal Structure Of A Protein Of Unknown Function
Yfbm From Escherichia Coli
Length = 167
Score = 28.1 bits (61), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 2/67 (2%)
Query: 223 SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGI--G 280
S PL+ +IH+ +S + I W H G+ G A D L + +H + G
Sbjct: 21 STEKPLMDNIHDTLSGLRRLDIDKRWDFLHFGLTGTSAFDPAKNDPLSRAVLGEHSLEDG 80
Query: 281 LTQLSGL 287
+ GL
Sbjct: 81 IDGFLGL 87
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
0.314 0.131 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,251,147
Number of Sequences: 62578
Number of extensions: 511551
Number of successful extensions: 898
Number of sequences better than 100.0: 86
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 80
Number of HSP's that attempted gapping in prelim test: 888
Number of HSP's gapped (non-prelim): 86
length of query: 405
length of database: 14,973,337
effective HSP length: 101
effective length of query: 304
effective length of database: 8,652,959
effective search space: 2630499536
effective search space used: 2630499536
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (25.0 bits)