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= psy10810
(786 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 555
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 38/124 (30%), Positives = 53/124 (42%), Gaps = 13/124 (10%)
Query: 519 YTDGSKNEQ---GVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKA 575
YTDGS N Q G +T K+ K+ N AEL A +L K
Sbjct: 440 YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQ---QAELEAFAMALTD----SGPKV 492
Query: 576 LIITDSLSCLQAITNM--FHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEA 633
II DS + + + E+ +V ++ EE+ E +I W P+H GI GN+ D
Sbjct: 493 NIIVDSQYVMGIVASQPTESESKIVNQIIEEMIKKE-AIYVAWVPAHKGIGGNQEVDHLV 551
Query: 634 KQAI 637
Q I
Sbjct: 552 SQGI 555
>pdb|2I5J|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Dhbnh, An Rnase H Inhibitor
Length = 552
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|1HYS|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With A Polypurine Tract Rna:dna
Length = 553
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|3QO9|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) In
Complex With Tsao-T, A Non-Nucleoside Rt Inhibitor
(Nnrti)
Length = 557
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 497
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 552
>pdb|3DLK|A Chain A, Crystal Structure Of An Engineered Form Of The Hiv-1
Reverse Transcriptase, Rt69a
Length = 556
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 442 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 496
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 497 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 551
>pdb|1DLO|A Chain A, Human Immunodeficiency Virus Type 1
pdb|1BQM|A Chain A, Hiv-1 RtHBY 097
Length = 556
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|3IG1|A Chain A, Hiv-1 Reverse Transcriptase With The Inhibitor Beta-
Thujaplicinol Bound At The Rnase H Active Site
Length = 555
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.9 bits (89), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 497
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 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 = 38.9 bits (89), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 497
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 552
>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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 38/130 (29%), Positives = 60/130 (46%), Gaps = 15/130 (11%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + +L A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTQLQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAK 634
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVD---- 549
Query: 635 QAINNDVTHH 644
+ ++ + HH
Sbjct: 550 KLVSAGIRHH 559
>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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 497
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 552
>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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|3HVT|A Chain A, Structural Basis Of Asymmetry In The Human
Immunodeficiency Virus Type 1 Reverse Transcriptase
Heterodimer
Length = 556
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 497
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 552
>pdb|1UWB|A Chain A, Tyr 181 Cys Hiv-1 Rt8-Cl Tibo
Length = 558
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 442 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 496
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 497 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 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 = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|4DG1|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase (Rt) With
Polymorphism Mutation K172a And K173a
Length = 549
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/116 (31%), Positives = 54/116 (46%), Gaps = 11/116 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAAD 630
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVD 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 = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 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 = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 497
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 552
>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 = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 38/117 (32%), Positives = 57/117 (48%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ L +++ G + I
Sbjct: 444 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIY---LALQDSG-LEVNI 498
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 499 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 553
>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 = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 38/130 (29%), Positives = 60/130 (46%), Gaps = 15/130 (11%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + +L A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTQLQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAK 634
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVD---- 549
Query: 635 QAINNDVTHH 644
+ ++ + HH
Sbjct: 550 KLVSAGIRHH 559
>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 = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 37/117 (31%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 497
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 552
>pdb|1BQN|A Chain A, Tyr 188 Leu Hiv-1 RtHBY 097
Length = 558
Score = 37.7 bits (86), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 36/117 (30%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GN+ D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNQQVDK 550
>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 = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 36/117 (30%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + +L A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTQLQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|1EET|A Chain A, Hiv-1 Reverse Transcriptase In Complex With The Inhibitor
Msc204
Length = 557
Score = 37.4 bits (85), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 36/117 (30%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + +L A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTQLQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.4 bits (85), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 36/117 (30%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + +L A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTQLQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 37/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + K K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNKGRQKVVPLTDTTNQKTQLQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDE-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|1S1X|A Chain A, Crystal Structure Of V108i Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 37.0 bits (84), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|1LWC|A Chain A, Crystal Structure Of M184v Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 37.0 bits (84), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|1LWE|A Chain A, Crystal Structure Of M41lT215Y MUTANT HIV-1 Reverse
Transcriptase (Rtmn) In Complex With Nevirapine
Length = 560
Score = 37.0 bits (84), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|3FFI|A Chain A, Hiv-1 Rt With Pyridone Non-Nucleoside Inhibitor
Length = 561
Score = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 442 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 495
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 551
>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 = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|1S1W|A Chain A, Crystal Structure Of V106a Mutant Hiv-1 Reverse
Transcriptase In Complex With Uc-781
Length = 560
Score = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 444 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 497
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 553
>pdb|1RT3|A Chain A, Azt Drug Resistant Hiv-1 Reverse Transcriptase Complexed
With 1051u91
Length = 560
Score = 37.0 bits (84), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|2YNF|A Chain A, Hiv-1 Reverse Transcriptase Y188l Mutant In Complex With
Inhibitor Gsk560
Length = 563
Score = 37.0 bits (84), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 444 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 497
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 553
>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 = 37.0 bits (84), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 444 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 498
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 499 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 553
>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 = 37.0 bits (84), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 495
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 496 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|1JLF|A Chain A, Crystal Structure Of Y188c Mutant Hiv-1 Reverse
Transcriptase In Complex With Nevirapine
Length = 560
Score = 37.0 bits (84), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 37.0 bits (84), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|3DRR|A Chain A, Hiv Reverse Transcriptase Y181c Mutant In Complex With
Inhibitor R8e
Length = 563
Score = 37.0 bits (84), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 444 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 497
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 553
>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 = 37.0 bits (84), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|3DMJ|A Chain A, Crystal Structure Of Hiv-1 V106a And Y181c Mutant Reverse
Transcriptase In Complex With Gw564511
Length = 560
Score = 36.6 bits (83), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 36/120 (30%), Positives = 52/120 (43%), Gaps = 17/120 (14%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ N E +G A + + K L + A AL S L +
Sbjct: 441 YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVN------ 494
Query: 575 ALIITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 --IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 36.6 bits (83), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 36/117 (30%), Positives = 55/117 (47%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ +L + + I
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIYLAL----QDSGLEVNI 497
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+T+S L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 498 VTNSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 552
>pdb|1RBS|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 36.2 bits (82), Expect = 0.076, Method: Composition-based stats.
Identities = 41/147 (27%), Positives = 60/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E AC+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--ACEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|1RBU|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 36.2 bits (82), Expect = 0.080, Method: Composition-based stats.
Identities = 41/145 (28%), Positives = 60/145 (41%), Gaps = 25/145 (17%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH----------ENPLVKRVQ--EELSSI--EPSIEF 614
E C+ ++ TDS Q IT H +N VK V + L + + I++
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADNKPVKNVDLWQRLDAALGQHQIKW 118
Query: 615 LWCPSHVGIAGNEAADEEAKQAINN 639
W H G NE DE A+ A N
Sbjct: 119 EWVKGHAGHPENERCDELARAAAMN 143
>pdb|3AA3|A Chain A, A52l E. Coli Rnase Hi
Length = 155
Score = 35.8 bits (81), Expect = 0.082, Method: Composition-based stats.
Identities = 41/147 (27%), Positives = 60/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL AL+ +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMALIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>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 = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 39/123 (31%), Positives = 58/123 (47%), Gaps = 11/123 (8%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ L +++ G + I
Sbjct: 17 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIY---LALQDSG-LEVNI 71
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAK 634
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 72 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKLVS 129
Query: 635 QAI 637
I
Sbjct: 130 AGI 132
>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 = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 39/123 (31%), Positives = 58/123 (47%), Gaps = 11/123 (8%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ L +++ G + I
Sbjct: 17 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIY---LALQDSG-LEVNI 71
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAK 634
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 72 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKLVS 129
Query: 635 QAI 637
I
Sbjct: 130 AGI 132
>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 = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 577 IITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 39/123 (31%), Positives = 58/123 (47%), Gaps = 11/123 (8%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ L +++ G + I
Sbjct: 15 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIY---LALQDSG-LEVNI 69
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAK 634
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 70 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKLVS 127
Query: 635 QAI 637
I
Sbjct: 128 AGI 130
>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 = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 39/123 (31%), Positives = 58/123 (47%), Gaps = 11/123 (8%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + K K L N + EL A+ L +++ G + I
Sbjct: 27 YVDGAANRETKLGKAGYVTNKGRQKVVPLT-NTTNQKTELQAIY---LALQDSG-LEVNI 81
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAK 634
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 82 VTDSQYALGIIQAQPDK-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKLVS 139
Query: 635 QAI 637
I
Sbjct: 140 AGI 142
>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 = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 41/147 (27%), Positives = 60/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS QAIT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQAITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|2VOA|A Chain A, Structure Of An Ap Endonuclease From Archaeoglobus
Fulgidus
pdb|2VOA|B Chain B, Structure Of An Ap Endonuclease From Archaeoglobus
Fulgidus
Length = 257
Score = 35.0 bits (79), Expect = 0.15, Method: Composition-based stats.
Identities = 39/174 (22%), Positives = 73/174 (41%), Gaps = 24/174 (13%)
Query: 1 MVNILQWNVNGVKNHLNDLTIKLRDINPKIICIQESHLKEEENFTLKGFNTVGTYEVILR 60
M+ I +NVN +++ L+ + L++ P I+C+QE+ + E F F+ +G Y V+
Sbjct: 1 MLKIATFNVNSIRSRLHIVIPWLKENKPDILCMQETKV-ENRKFPEADFHRIG-YHVVFS 58
Query: 61 QLHKWNMRGHLPIFLSKYMDPRSFKIRLNNSILSENFSI---VCGI-------PQGGVVS 110
+G + ++ +P L++ E+ I + GI PQG +
Sbjct: 59 -----GSKGRNGVAIASLEEPEDVSFGLDSEPKDEDRLIRAKIAGIDVINTYVPQGFKID 113
Query: 111 GTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSED 164
+ + + H L ++ FA++ D N + E ID S D
Sbjct: 114 SEKYQYKLQWLERLYH-YLQKTVDFRSFAVWCGDMN------VAPEPIDVHSPD 160
>pdb|3AA2|A Chain A, A52i E. Coli Rnase Hi
Length = 155
Score = 35.0 bits (79), Expect = 0.16, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 60/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A++ +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAIIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|3AA4|A Chain A, A52v E.Coli Rnase Hi
Length = 155
Score = 34.7 bits (78), Expect = 0.20, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 60/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A++ +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAVIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>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 = 0.22, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 577 IITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEA 633
I+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 73 IVTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDKLV 130
Query: 634 KQAI 637
I
Sbjct: 131 SAGI 134
>pdb|3AA5|X Chain X, A52f E.Coli Rnase Hi
Length = 155
Score = 34.7 bits (78), Expect = 0.22, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAFIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|2OPR|A Chain A, Crystal Structure Of K101e Mutant Hiv-1 Reverse
Transcriptase In Complex With Gw420867x
Length = 547
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 34/113 (30%), Positives = 53/113 (46%), Gaps = 11/113 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 440 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 494
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNE 627
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GNE
Sbjct: 495 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNE 545
>pdb|1RBR|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 34.3 bits (77), Expect = 0.30, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--PCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|1RCH|A Chain A, Solution Nmr Structure Of Ribonuclease Hi From Escherichia
Coli, 8 Structures
pdb|1RDD|A Chain A, Crystal Structure Of Escherichia Coli Rnase Hi In Complex
With Mg2+ At 2.8 Angstroms Resolution: Proof For A
Single Mg2+ Site
pdb|2RN2|A Chain A, Structural Details Of Ribonuclease H From Escherichia Coli
As Refined To An Atomic Resolution
Length = 155
Score = 33.9 bits (76), Expect = 0.39, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|1LAW|A Chain A, Stabilization Of Escherichia Coli Ribonuclease Hi By
Cavity- Filling Mutations Within A Hydrophobic Core
Length = 155
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYIRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|1LAV|A Chain A, Stabilization Of Escherichia Coli Ribonuclease Hi By
Cavity- Filling Mutations Within A Hydrophobic Core
Length = 155
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYLRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|1RBT|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 40/145 (27%), Positives = 59/145 (40%), Gaps = 25/145 (17%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH----------ENPLVKRVQ--EELSSI--EPSIEF 614
E C+ ++ TDS Q IT H + VK V + L + + I++
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADGKPVKNVDLWQRLDAALGQHQIKW 118
Query: 615 LWCPSHVGIAGNEAADEEAKQAINN 639
W H G NE DE A+ A N
Sbjct: 119 EWVKGHAGHPENERCDELARAAAMN 143
>pdb|1RBV|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 33.5 bits (75), Expect = 0.52, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 58/147 (39%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFHE-----------NP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADAKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>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 = 33.1 bits (74), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 577 IITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I+T+S L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 495 IVTNSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>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 = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 33/117 (28%), Positives = 51/117 (43%), Gaps = 11/117 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNA---SIFHAELFALLQSLLTIKELGACK 574
Y DG+ + E +G A + K K L + A AL S L + + A +
Sbjct: 441 YVDGAASRETKLGKAGYVTNKGRQKVVTLTDTTNQKTELQAIHLALQDSGLEVNIVTASQ 500
Query: 575 ALIITDSLSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADE 631
+L +QA + E+ LV ++ E+L E + W P+H GI GNE D+
Sbjct: 501 Y-----ALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGNEQVDK 550
>pdb|2Z1H|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
Mutant(Q4rT92KQ105KQ113RQ115KN143KT145K)
Length = 155
Score = 33.1 bits (74), Expect = 0.59, Method: Composition-based stats.
Identities = 40/143 (27%), Positives = 57/143 (39%), Gaps = 29/143 (20%)
Query: 516 IKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIKE 569
++I+TDGS G G L EK + + N + EL A + +L +KE
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALKE 61
Query: 570 LGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSIE 613
C+ ++ TDS Q IT H + P L KR+ L I+
Sbjct: 62 --HCEVILSTDSQYVRQGITQWIHNWKKRGWKKADKKPVKNVDLWKRLDAALG--RHKIK 117
Query: 614 FLWCPSHVGIAGNEAADEEAKQA 636
+ W H G NE DE A+ A
Sbjct: 118 WEWVKGHAGHPENERCDELARAA 140
>pdb|1RNH|A Chain A, Structure Of Ribonuclease H Phased At 2 Angstroms
Resolution By Mad Analysis Of The Selenomethionyl
Protein
Length = 155
Score = 33.1 bits (74), Expect = 0.62, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 58/147 (39%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNN---RXELXAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAXN 143
>pdb|2OKX|A Chain A, Crystal Structure Of Gh78 Family Rhamnosidase Of Bacillus
Sp. Gl1 At 1.9 A
pdb|2OKX|B Chain B, Crystal Structure Of Gh78 Family Rhamnosidase Of Bacillus
Sp. Gl1 At 1.9 A
Length = 956
Score = 33.1 bits (74), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 9/94 (9%)
Query: 584 CLQAITNMFHENPL-VKRVQEELSSIEPSIEFLW---CPSHVGIAGNEAADEEAKQAINN 639
CL + E PL + +V SS+ P+ F W C + GNEA A+ +
Sbjct: 600 CLNLVPGSADETPLYLDQVPSAWSSVIPNWTFFWILACREYAAHTGNEAFAARIWPAVKH 659
Query: 640 DVTHHELSLDEIKTIIKKKYLEEWN-TTWLPKDR 672
+TH+ +D+ + + WN W P D+
Sbjct: 660 TLTHYLEHIDDSGLL----NMAGWNLLDWAPIDQ 689
>pdb|1GOC|A Chain A, Cooperative Stabilization Of Escherichia Coli Ribonuclease
Hi By Insertion Of Gly-80b And Gly-77-> Ala Substitution
Length = 156
Score = 33.1 bits (74), Expect = 0.67, Method: Composition-based stats.
Identities = 40/148 (27%), Positives = 59/148 (39%), Gaps = 30/148 (20%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFHEN-----------------PLVKRVQEELSSIEPS 611
E C+ ++ TDS QAIT + N L +R+ L +
Sbjct: 61 E--HCEVILSTDSQYVRQAITQGWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQ 116
Query: 612 IEFLWCPSHVGIAGNEAADEEAKQAINN 639
I++ W H G NE DE A+ A N
Sbjct: 117 IKWEWVKGHAGHPENERCDELARAAAMN 144
>pdb|2OPP|A Chain A, Crystal Structure Of Hiv-1 Reverse Transcriptase In
Complex With Gw420867x
Length = 542
Score = 32.7 bits (73), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 52/112 (46%), Gaps = 11/112 (9%)
Query: 519 YTDGSKN-EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALI 577
Y DG+ N E +G A + + K L + + EL A+ +L + + I
Sbjct: 438 YVDGAANRETKLGKAGYVTNRGRQKVVTLT-DTTNQKTELQAIYLAL----QDSGLEVNI 492
Query: 578 ITDS---LSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGN 626
+TDS L +QA + E+ LV ++ E+L E + W P+H GI GN
Sbjct: 493 VTDSQYALGIIQAQPDQ-SESELVNQIIEQLIKKE-KVYLAWVPAHKGIGGN 542
>pdb|2Z1G|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105K)
Length = 155
Score = 32.7 bits (73), Expect = 0.84, Method: Composition-based stats.
Identities = 40/146 (27%), Positives = 59/146 (40%), Gaps = 29/146 (19%)
Query: 516 IKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIKE 569
++I+TDGS G G L EK + + N + EL A + +L +KE
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYERTTNNRM---ELMAAIVALEALKE 61
Query: 570 LGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSIE 613
C+ ++ TDS + IT H + P L KR+ L + I+
Sbjct: 62 --HCEVILSTDSHYVRKGITEWIHNWKKRGWKKADKKPVKNVDLWKRLDAALG--QHQIK 117
Query: 614 FLWCPSHVGIAGNEAADEEAKQAINN 639
+ W H G NE DE A+ A N
Sbjct: 118 WEWVKGHAGHPENERCDELARAAAMN 143
>pdb|1RDB|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
From Escherichia Coli
Length = 155
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 39/147 (26%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + +L A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---QLMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|3HYF|A Chain A, Crystal Structure Of Hiv-1 Rnase H P15 With Engineered E.
Coli Loop And Active Site Inhibitor
pdb|3QIN|A Chain A, Crystal Structure Of Hiv-1 Rnase H P15 With Engineered E.
Coli Loop And Pyrimidinol Carboxylic Acid Inhibitor
pdb|3QIO|A Chain A, Crystal Structure Of Hiv-1 Rnase H With Engineered E. Coli
Loop And N- Hydroxy Quinazolinedione Inhibitor
Length = 150
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 17/77 (22%)
Query: 577 IITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSIEFLWCPSH 620
I+TDS L IT H + P LV ++ E+L E + W P+H
Sbjct: 70 IVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKE-KVYLAWVPAH 128
Query: 621 VGIAGNEAADEEAKQAI 637
GI GNE D+ I
Sbjct: 129 KGIGGNEQVDKLVSAGI 145
>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 = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGSK----NEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E + ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HAEVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE ADE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERADELARAAAMN 143
>pdb|1F21|A Chain A, Divalent Metal Cofactor Binding In The Kinetic Folding
Trajectory Of E. Coli Ribonuclease Hi
Length = 155
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGSK----NEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E + ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE ADE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERADELARAAAMN 143
>pdb|1RDA|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
From Escherichia Coli
Length = 155
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 39/147 (26%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+T+GS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTNGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|1RDC|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
From Escherichia Coli
Length = 155
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 39/147 (26%), Positives = 59/147 (40%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ T+S Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTNSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|2Z1I|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105KQ113RQ115K)
pdb|2Z1I|B Chain B, Crystal Structure Of E.Coli Rnase Hi Surface Charged
Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105KQ113RQ115K)
Length = 155
Score = 32.0 bits (71), Expect = 1.5, Method: Composition-based stats.
Identities = 40/146 (27%), Positives = 58/146 (39%), Gaps = 29/146 (19%)
Query: 516 IKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIKE 569
++I+TDGS G G L EK + + N + EL A + +L +KE
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYERTTNNRM---ELMAAIVALEALKE 61
Query: 570 LGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSIE 613
C+ ++ TDS + IT H + P L KR+ L I+
Sbjct: 62 --HCEVILSTDSHYVRKGITEWIHNWKKRGWKKADKKPVKNVDLWKRLDAALG--RHKIK 117
Query: 614 FLWCPSHVGIAGNEAADEEAKQAINN 639
+ W H G NE DE A+ A N
Sbjct: 118 WEWVKGHAGHPENERCDELARAAAMN 143
>pdb|1GOA|A Chain A, Cooperative Stabilization Of Escherichia Coli Ribonuclease
Hi By Insertion Of Gly-80b And Gly-77-> Ala Substitution
Length = 156
Score = 31.6 bits (70), Expect = 2.0, Method: Composition-based stats.
Identities = 39/148 (26%), Positives = 58/148 (39%), Gaps = 30/148 (20%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFHEN-----------------PLVKRVQEELSSIEPS 611
E C+ ++ TDS Q IT + N L +R+ L +
Sbjct: 61 E--HCEVILSTDSQYVRQGITQGWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQ 116
Query: 612 IEFLWCPSHVGIAGNEAADEEAKQAINN 639
I++ W H G NE DE A+ A N
Sbjct: 117 IKWEWVKGHAGHPENERCDELARAAAMN 144
>pdb|1WSH|A Chain A, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aK87A)
pdb|1WSH|B Chain B, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aK87A)
pdb|1WSH|C Chain C, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aK87A)
pdb|1WSH|D Chain D, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aK87A)
pdb|1WSE|A Chain A, Co-Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48a) With Mn2+
pdb|1WSE|B Chain B, Co-Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48a) With Mn2+
Length = 155
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 39/147 (26%), Positives = 58/147 (39%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + L A + +L +K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ALMAAIVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E C+ ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HCEVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERCDELARAAAMN 143
>pdb|2Z1J|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105KQ113RQ115KN143K
T145K)
Length = 155
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 39/143 (27%), Positives = 57/143 (39%), Gaps = 29/143 (20%)
Query: 516 IKIYTDGS----KNEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIKE 569
++I+TDGS G G L EK + + N + EL A + +L +KE
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYERTTNNRM---ELMAAIVALEALKE 61
Query: 570 LGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSIE 613
C+ ++ TDS + IT H + P L KR+ L I+
Sbjct: 62 --HCEVILSTDSHYVRKGITEWIHNWKKRGWKKADKKPVKNVDLWKRLDAALG--RHKIK 117
Query: 614 FLWCPSHVGIAGNEAADEEAKQA 636
+ W H G NE DE A+ A
Sbjct: 118 WEWVKGHAGHPENERCDELARAA 140
>pdb|1JXB|A Chain A, I53a, A Point Mutant Of The Cysteine-Free Variant Of E.
Coli Rnase Hi
Length = 155
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 40/147 (27%), Positives = 58/147 (39%), Gaps = 29/147 (19%)
Query: 515 HIKIYTDGSK----NEQGVGCALTIP--EKNIAKRFGLNKNASIFHAELFALLQSLLTIK 568
++I+TDGS G G L EK + + N + EL A +L +K
Sbjct: 4 QVEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRM---ELMAAAVALEALK 60
Query: 569 ELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVKRVQEELSSIEPSI 612
E + ++ TDS Q IT H + P L +R+ L + I
Sbjct: 61 E--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG--QHQI 116
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE ADE A+ A N
Sbjct: 117 KWEWVKGHAGHPENERADELARAAAMN 143
>pdb|2V0S|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Lr1) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 236
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 15/92 (16%)
Query: 2 VNILQWNVNG----VKNHLNDLTIKLRDINPKIICIQESHL--KEEENFTLKGFNTVGTY 55
+ IL N+NG +K H IK +D P + CIQE+HL ++ +KG+ + Y
Sbjct: 8 ITILTLNINGLNSAIKRHRLASWIKSQD--PSVCCIQETHLTCRDTHRLKIKGWRKI--Y 63
Query: 56 EVILRQLHKWNMRGHLPIFLSKYMDPRSFKIR 87
+ +Q + + I +S D + KI+
Sbjct: 64 QANGKQ-----KKAGVAILVSDKTDFKPTKIK 90
>pdb|1VYB|A Chain A, Endonuclease Domain Of Human Line1 Orf2p
pdb|1VYB|B Chain B, Endonuclease Domain Of Human Line1 Orf2p
Length = 238
Score = 30.4 bits (67), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 2 VNILQWNVNG----VKNHLNDLTIKLRDINPKIICIQESHL--KEEENFTLKGFNTV 52
+ IL N+NG +K H IK +D P + CIQE+HL ++ +KG+ +
Sbjct: 8 ITILTLNINGLNSAIKRHRLASWIKSQD--PSVCCIQETHLTCRDTHRLKIKGWRKI 62
>pdb|2V0R|A Chain A, Crystal Structure Of A Hairpin Exchange Variant (Ltx) Of
The Targeting Line-1 Retrotransposon Endonuclease
pdb|2V0R|B Chain B, Crystal Structure Of A Hairpin Exchange Variant (Ltx) Of
The Targeting Line-1 Retrotransposon Endonuclease
Length = 240
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 2 VNILQWNVNG----VKNHLNDLTIKLRDINPKIICIQESHL--KEEENFTLKGFNTV 52
+ IL N+NG +K H IK +D P + CIQE+HL ++ +KG+ +
Sbjct: 8 ITILTLNINGLNSAIKRHRLASWIKSQD--PSVCCIQETHLTCRDTHRLKIKGWRKI 62
>pdb|1JL1|A Chain A, D10a E. Coli Ribonuclease Hi
Length = 155
Score = 29.6 bits (65), Expect = 7.3, Method: Composition-based stats.
Identities = 29/100 (29%), Positives = 42/100 (42%), Gaps = 20/100 (20%)
Query: 556 ELFALLQSLLTIKELGACKALIITDSLSCLQAITNMFH-----------ENP-----LVK 599
EL A + +L +KE + ++ TDS Q IT H + P L +
Sbjct: 48 ELMAAIVALEALKE--HAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQ 105
Query: 600 RVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAINN 639
R+ L + I++ W H G NE ADE A+ A N
Sbjct: 106 RLDAALG--QHQIKWEWVKGHAGHPENERADELARAAAMN 143
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
0.319 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,690,982
Number of Sequences: 62578
Number of extensions: 930019
Number of successful extensions: 2366
Number of sequences better than 100.0: 109
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 108
Number of HSP's that attempted gapping in prelim test: 2299
Number of HSP's gapped (non-prelim): 174
length of query: 786
length of database: 14,973,337
effective HSP length: 107
effective length of query: 679
effective length of database: 8,277,491
effective search space: 5620416389
effective search space used: 5620416389
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)