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= psy16039
(586 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>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 = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 479 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 530
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 531 KEKVYLAWVPAHKGIGGNEQVD 552
>pdb|1HYS|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With A Polypurine Tract Rna:dna
Length = 553
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>pdb|4DG1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Polymorphism Mutation K172a And K173a
Length = 549
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 477 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 528
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 529 KEKVYLAWVPAHKGIGGNEQVD 550
>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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 478 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 529
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 551
>pdb|1DLO|A Chain A, Human Immunodeficiency Virus Type 1
pdb|1BQM|A Chain A, Hiv-1 RtHBY 097
Length = 556
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 478 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 529
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 551
>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta-
Thujaplicinol Bound At The Rnase H Active Site
Length = 555
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1
Reverse Transcriptase, Rt69a
Length = 556
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 477 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 528
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 529 KEKVYLAWVPAHKGIGGNEQVD 550
>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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 478 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 529
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 551
>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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 478 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 529
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 478 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 529
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>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 = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 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 = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>pdb|1UWB|A Chain A, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo
Length = 558
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>pdb|3HVT|A Chain A, Structural Basis Of Asymmetry In The Human
Immunodeficiency Virus Type 1 Reverse Transcriptase
Heterodimer
Length = 556
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>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 = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 476 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 527
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 528 KEKVYLAWVPAHKGIGGNEQVD 549
>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 = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 478 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 529
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 551
>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 = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 449 SSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDC 506
+EL AI L +++ +++DS AL I K++ LV+ + +E
Sbjct: 478 KTELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQI----IEQLIK 529
Query: 507 GKNLNFVWCPSHCGITGNELVD 528
+ + W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 551
>pdb|3U1N|A Chain A, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|B Chain B, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|C Chain C, Structure Of The Catalytic Core Of Human Samhd1
pdb|3U1N|D Chain D, Structure Of The Catalytic Core Of Human Samhd1
Length = 528
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 360 DSEFVPFTRPRPPWSFQVPSIDFSLHLDNKDNIPPIVFQ 398
D F+P RP W+ + S+ HL N + I P+ Q
Sbjct: 120 DGRFIPLARPEVKWTHEQGSVXXFEHLINSNGIKPVXEQ 158
>pdb|3PL6|A Chain A, Structure Of Autoimmune Tcr Hy.1b11 In Complex With
Hla-Dq1 And Mbp 85-99
Length = 194
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 456 LLCVKNLIFLPSTNFTLISDSMSALLAISNC----KNDHPLVSLVYTTWLEAKD 505
L+C+ + IF P N T +S+ S +S K+DH + Y T+L + D
Sbjct: 108 LICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFLPSAD 161
>pdb|1UVQ|A Chain A, Crystal Structure Of Hla-Dq0602 In Complex With A
Hypocretin Peptide
Length = 197
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 456 LLCVKNLIFLPSTNFTLISDSMSALLAISNC----KNDHPLVSLVYTTWLEAKD 505
L+C+ + IF P N T +S+ S +S K+DH + Y T+L + D
Sbjct: 108 LICLVDNIFPPVVNITWLSNGQSVTEGVSETSFLSKSDHSFFKISYLTFLPSAD 161
>pdb|2NNA|A Chain A, Structure Of The Mhc Class Ii Molecule Hla-Dq8 Bound With
A Deamidated Gluten Peptide
Length = 184
Score = 30.8 bits (68), Expect = 2.1, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 456 LLCVKNLIFLPSTNFTLISDSMSALLAISN----CKNDHPLVSLVYTTWLEAKD 505
L+C+ + IF P N T +S+ S +S K+DH + Y T+L + D
Sbjct: 108 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSAD 161
>pdb|1S9V|A Chain A, Crystal Structure Of Hla-Dq2 Complexed With Deamidated
Gliadin Peptide
pdb|1S9V|D Chain D, Crystal Structure Of Hla-Dq2 Complexed With Deamidated
Gliadin Peptide
Length = 193
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 455 ILLCVKNLIFLPSTNFTLISDSMSALLAISNC----KNDHPLVSLVYTTWL----EAKDC 506
IL+C+ + IF P N T +S+ S +S K+DH + Y T L E+ DC
Sbjct: 106 ILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDC 165
>pdb|1JK8|A Chain A, Crystal Structure Of A Human Insulin Peptide-Hla-Dq8
Complex
Length = 181
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 456 LLCVKNLIFLPSTNFTLISDSMSALLAISNC----KNDHPLVSLVYTTWLEAKD 505
L+C+ + IF P N T +S+ S +S K+DH + Y T+L + D
Sbjct: 105 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDD 158
>pdb|4GG6|A Chain A, Protein Complex
pdb|4GG6|C Chain C, Protein Complex
Length = 192
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 456 LLCVKNLIFLPSTNFTLISDSMSALLAISNC----KNDHPLVSLVYTTWLEAKD 505
L+C+ + IF P N T +S+ S +S K+DH + Y T+L + D
Sbjct: 108 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSAD 161
>pdb|4D8P|A Chain A, Structural And Functional Studies Of The Trans-Encoded
Hla-Dq2.3 (Dqa103:01DQB102:01) MOLECULE
pdb|4D8P|C Chain C, Structural And Functional Studies Of The Trans-Encoded
Hla-Dq2.3 (Dqa103:01DQB102:01) MOLECULE
Length = 213
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 456 LLCVKNLIFLPSTNFTLISDSMSALLAISNC----KNDHPLVSLVYTTWLEAKD 505
L+C+ + IF P N T +S+ S +S K+DH + Y T+L + D
Sbjct: 108 LICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSAD 161
>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 = 29.6 bits (65), Expect = 4.7, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 450 SELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCG 507
+EL AI L +++ +++DS AL I K++ LV+ + ++ +
Sbjct: 51 TELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKE--- 103
Query: 508 KNLNFVWCPSHCGITGNELVD 528
+ W P+H GI GNE VD
Sbjct: 104 -KVYLAWVPAHKGIGGNEQVD 123
>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 = 29.6 bits (65), Expect = 4.7, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 450 SELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCG 507
+EL AI L +++ +++DS AL I K++ LV+ + ++ +
Sbjct: 63 TELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKE--- 115
Query: 508 KNLNFVWCPSHCGITGNELVD 528
+ W P+H GI GNE VD
Sbjct: 116 -KVYLAWVPAHKGIGGNEQVD 135
>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 = 29.6 bits (65), Expect = 4.7, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 450 SELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCG 507
+EL AI L +++ +++DS AL I K++ LV+ + ++ +
Sbjct: 53 TELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKE--- 105
Query: 508 KNLNFVWCPSHCGITGNELVD 528
+ W P+H GI GNE VD
Sbjct: 106 -KVYLAWVPAHKGIGGNEQVD 125
>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 = 29.6 bits (65), Expect = 4.7, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 450 SELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC--KNDHPLVSLVYTTWLEAKDCG 507
+EL AI L +++ +++DS AL I K++ LV+ + ++ +
Sbjct: 53 TELQAIYLALQD----SGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKE--- 105
Query: 508 KNLNFVWCPSHCGITGNELVD 528
+ W P+H GI GNE VD
Sbjct: 106 -KVYLAWVPAHKGIGGNEQVD 125
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
0.323 0.137 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,528,229
Number of Sequences: 62578
Number of extensions: 671013
Number of successful extensions: 1161
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 39
Number of HSP's that attempted gapping in prelim test: 1160
Number of HSP's gapped (non-prelim): 40
length of query: 586
length of database: 14,973,337
effective HSP length: 104
effective length of query: 482
effective length of database: 8,465,225
effective search space: 4080238450
effective search space used: 4080238450
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)