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= psy3458
(151 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QKB|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 20-Mer RnaDNA HYBRID
pdb|2QKB|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 20-Mer RnaDNA HYBRID
Length = 154
Score = 122 bits (307), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 61/145 (42%), Positives = 90/145 (62%), Gaps = 1/145 (0%)
Query: 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
+ VVV+TDG C NG+ AG GVY+G +PLNV ++ GR TN AEI A A++QA
Sbjct: 6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQA 65
Query: 65 KSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESV 124
K+ NI+++ + ++S F I + W+ W+ NGW+ + GK V NKE+ L ++ Q +
Sbjct: 66 KTQNINKLVLYTNSXFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVA-LERLTQGXDI 124
Query: 125 KWEFVPGHGNSHGNMKADEMARDAA 149
+W VPGH GN +AD +AR+ A
Sbjct: 125 QWXHVPGHSGFIGNEEADRLAREGA 149
>pdb|2QK9|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 18-Mer RnaDNA HYBRID
pdb|2QKK|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|E Chain E, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|F Chain F, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|I Chain I, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|J Chain J, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|M Chain M, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|N Chain N, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|R Chain R, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|S Chain S, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
pdb|2QKK|W Chain W, Human Rnase H Catalytic Domain Mutant D210n In Complex
With 14-Mer RnaDNA HYBRID
Length = 154
Score = 122 bits (306), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 61/145 (42%), Positives = 90/145 (62%), Gaps = 1/145 (0%)
Query: 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
+ VVV+TDG C NG+ AG GVY+G +PLNV ++ GR TN AEI A A++QA
Sbjct: 6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQA 65
Query: 65 KSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESV 124
K+ NI+++ + ++S F I + W+ W+ NGW+ + GK V NKE+ L ++ Q +
Sbjct: 66 KTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVA-LERLTQGMDI 124
Query: 125 KWEFVPGHGNSHGNMKADEMARDAA 149
+W VPGH GN +AD +AR+ A
Sbjct: 125 QWMHVPGHSGFIGNEEADRLAREGA 149
>pdb|1RBT|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 87.8 bits (216), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 54/144 (37%), Positives = 77/144 (53%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ ADGKPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADGKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|2YV0|X Chain X, Structural And Thermodynamic Analyses Of E. Coli
Ribonuclease Hi Variant With Quintuple Thermostabilizing
Mutations
Length = 155
Score = 87.8 bits (216), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 54/144 (37%), Positives = 77/144 (53%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G A Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYAAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ ADGKPV+N + Q L +GQ + +K
Sbjct: 61 EPC--EVILSTDSQYLRQGITQWIHNWKKRGWKTADGKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + E+AR AA
Sbjct: 118 WEWVKGHAGHPENERCHELARAAA 141
>pdb|1RBS|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 87.4 bits (215), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 54/144 (37%), Positives = 77/144 (53%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
A V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EAC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|2Z1G|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105K)
Length = 155
Score = 86.7 bits (213), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 52/143 (36%), Positives = 75/143 (52%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+C N G Y G + + R TNN E+ AI AL+ K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYE---RTTNNRMELMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DS ++ K + EW+ W+ GW+KAD KPV+N + + L +GQ + +KW
Sbjct: 62 HC--EVILSTDSHYVRKGITEWIHNWKKRGWKKADKKPVKNVDLWKRLDAALGQHQ-IKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N + DE+AR AA
Sbjct: 119 EWVKGHAGHPENERCDELARAAA 141
>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 = 86.3 bits (212), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 53/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQAITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1LAV|A Chain A, Stabilization Of Escherichia Coli Ribonuclease Hi By
Cavity- Filling Mutations Within A Hydrophobic Core
Length = 155
Score = 85.9 bits (211), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 53/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYLRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1RBV|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 85.9 bits (211), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 53/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADAKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1RBR|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 53/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EPC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1LAW|A Chain A, Stabilization Of Escherichia Coli Ribonuclease Hi By
Cavity- Filling Mutations Within A Hydrophobic Core
Length = 155
Score = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 53/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYIRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1RBU|A Chain A, Structural Study Of Mutants Of Escherichia Coli
Ribonuclease Hi With Enhanced Thermostability
Length = 155
Score = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 53/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADNKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1RNH|A Chain A, Structure Of Ribonuclease H Phased At 2 Angstroms
Resolution By Mad Analysis Of The Selenomethionyl
Protein
Length = 155
Score = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 53/143 (37%), Positives = 76/143 (53%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRXELXAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +KW
Sbjct: 62 HC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N + DE+AR AA
Sbjct: 119 EWVKGHAGHPENERCDELARAAA 141
>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 = 85.1 bits (209), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 53/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>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 = 85.1 bits (209), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 51/143 (35%), Positives = 74/143 (51%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+C N G Y G + + R TNN E+ AI AL+ K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYE---RTTNNRMELMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DS ++ K + EW+ W+ GW+KAD KPV+N + + L +G+ +KW
Sbjct: 62 HC--EVILSTDSHYVRKGITEWIHNWKKRGWKKADKKPVKNVDLWKRLDAALGR-HKIKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N + DE+AR AA
Sbjct: 119 EWVKGHAGHPENERCDELARAAA 141
>pdb|2Z1J|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105KQ113RQ115KN143K
T145K)
Length = 155
Score = 84.7 bits (208), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 51/143 (35%), Positives = 74/143 (51%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+C N G Y G + + R TNN E+ AI AL+ K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYE---RTTNNRMELMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DS ++ K + EW+ W+ GW+KAD KPV+N + + L +G+ +KW
Sbjct: 62 HC--EVILSTDSHYVRKGITEWIHNWKKRGWKKADKKPVKNVDLWKRLDAALGR-HKIKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N + DE+AR AA
Sbjct: 119 EWVKGHAGHPENERCDELARAAA 141
>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 = 84.7 bits (208), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 53/143 (37%), Positives = 77/143 (53%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+ N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 5 VEIFTDGSALGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++ + + +W+ W++ GW+ AD KPV+N + Q L +GQ + +KW
Sbjct: 62 HA--EVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQ-IKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N +ADE+AR AA
Sbjct: 119 EWVKGHAGHPENERADELARAAA 141
>pdb|2Z1H|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
Mutant(Q4rT92KQ105KQ113RQ115KN143KT145K)
Length = 155
Score = 84.0 bits (206), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 50/143 (34%), Positives = 74/143 (51%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+C N G Y G + R TNN E+ AI AL+ K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAG---YTRTTNNRMELMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++ + + +W+ W+ GW+KAD KPV+N + + L +G+ +KW
Sbjct: 62 HC--EVILSTDSQYVRQGITQWIHNWKKRGWKKADKKPVKNVDLWKRLDAALGR-HKIKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N + DE+AR AA
Sbjct: 119 EWVKGHAGHPENERCDELARAAA 141
>pdb|1F21|A Chain A, Divalent Metal Cofactor Binding In The Kinetic Folding
Trajectory Of E. Coli Ribonuclease Hi
Length = 155
Score = 84.0 bits (206), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 53/143 (37%), Positives = 76/143 (53%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+ N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 5 VEIFTDGSALGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +KW
Sbjct: 62 HA--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N +ADE+AR AA
Sbjct: 119 EWVKGHAGHPENERADELARAAA 141
>pdb|1RDB|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
From Escherichia Coli
Length = 155
Score = 84.0 bits (206), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN ++ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMQLMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|3AA4|A Chain A, A52v E.Coli Rnase Hi
Length = 155
Score = 83.6 bits (205), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 75/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ I AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAVIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>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 = 83.6 bits (205), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN + AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMALMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W++ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|3AA2|A Chain A, A52i E. Coli Rnase Hi
Length = 155
Score = 83.6 bits (205), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 75/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ I AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAIIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|3AA3|A Chain A, A52l E. Coli Rnase Hi
Length = 155
Score = 83.6 bits (205), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 75/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ I AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMALIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1RDA|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
From Escherichia Coli
Length = 155
Score = 83.2 bits (204), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FT+G+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTNGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1RDC|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
From Escherichia Coli
Length = 155
Score = 83.2 bits (204), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + ++SQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTNSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1KVC|A Chain A, E. Coli Ribonuclease Hi D134n Mutant
Length = 155
Score = 83.2 bits (204), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + +E+AR AA
Sbjct: 118 WEWVKGHAGHPENERCNELARAAA 141
>pdb|3AA5|X Chain X, A52f E.Coli Rnase Hi
Length = 155
Score = 82.8 bits (203), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 75/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ I AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAFIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + DE+AR AA
Sbjct: 118 WEWVKGHAGHPENERCDELARAAA 141
>pdb|1WSF|A Chain A, Co-crystal Structure Of E.coli Rnase Hi Active Site Mutant
(d134a*) With Mn2+
pdb|1WSF|B Chain B, Co-crystal Structure Of E.coli Rnase Hi Active Site Mutant
(d134a*) With Mn2+
pdb|1WSF|C Chain C, Co-crystal Structure Of E.coli Rnase Hi Active Site Mutant
(d134a*) With Mn2+
pdb|1WSF|D Chain D, Co-crystal Structure Of E.coli Rnase Hi Active Site Mutant
(d134a*) With Mn2+
Length = 155
Score = 82.8 bits (203), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W++ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + E+AR AA
Sbjct: 118 WEWVKGHAGHPENERCAELARAAA 141
>pdb|1KVB|A Chain A, E. Coli Ribonuclease Hi D134h Mutant
Length = 155
Score = 82.4 bits (202), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 52/143 (36%), Positives = 75/143 (52%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +KW
Sbjct: 62 HC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N + E+AR AA
Sbjct: 119 EWVKGHAGHPENERCHELARAAA 141
>pdb|1WSJ|A Chain A, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(K87aH124A)
pdb|1WSJ|B Chain B, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(K87aH124A)
pdb|1WSJ|C Chain C, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(K87aH124A)
pdb|1WSJ|D Chain D, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(K87aH124A)
pdb|1WSJ|E Chain E, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(K87aH124A)
pdb|1WSJ|F Chain F, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(K87aH124A)
pdb|1WSJ|G Chain G, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(K87aH124A)
pdb|1WSJ|H Chain H, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(K87aH124A)
Length = 155
Score = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 76/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W++ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V G N + DE+AR AA
Sbjct: 118 WEWVKGAAGHPENERCDELARAAA 141
>pdb|1KVA|A Chain A, E. Coli Ribonuclease Hi D134a Mutant
Length = 155
Score = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 52/144 (36%), Positives = 75/144 (52%), Gaps = 6/144 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +K
Sbjct: 61 EHC--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IK 117
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N + E+AR AA
Sbjct: 118 WEWVKGHAGHPENERCAELARAAA 141
>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 = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 54/145 (37%), Positives = 76/145 (52%), Gaps = 7/145 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCV-QEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESV 124
V + +DSQ++ + + Q W+ W+ GW+ AD KPV+N + Q L +GQ + +
Sbjct: 61 EHC--EVILSTDSQYVRQAITQGWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-I 117
Query: 125 KWEFVPGHGNSHGNMKADEMARDAA 149
KWE+V GH N + DE+AR AA
Sbjct: 118 KWEWVKGHAGHPENERCDELARAAA 142
>pdb|1JXB|A Chain A, I53a, A Point Mutant Of The Cysteine-Free Variant Of E.
Coli Rnase Hi
Length = 155
Score = 81.6 bits (200), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 52/143 (36%), Positives = 75/143 (52%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+ N G Y G + AG R TNN E+ A AL+ K
Sbjct: 5 VEIFTDGSALGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAAVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +KW
Sbjct: 62 HA--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N +ADE+AR AA
Sbjct: 119 EWVKGHAGHPENERADELARAAA 141
>pdb|1WSI|A Chain A, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aK87AD134N)
pdb|1WSI|B Chain B, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aK87AD134N)
pdb|1WSI|C Chain C, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aK87AD134N)
pdb|1WSI|D Chain D, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aK87AD134N)
pdb|1WSG|A Chain A, Co-Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aD134N) WITH MN2+
pdb|1WSG|B Chain B, Co-Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aD134N) WITH MN2+
pdb|1WSG|C Chain C, Co-Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aD134N) WITH MN2+
pdb|1WSG|D Chain D, Co-Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
(E48aD134N) WITH MN2+
Length = 155
Score = 81.3 bits (199), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 51/143 (35%), Positives = 76/143 (53%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+C N G Y G + AG R TNN + AI AL+ K
Sbjct: 5 VEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMALMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++ + + +W+ W++ GW+ AD KPV+N + Q L +GQ + +KW
Sbjct: 62 HC--EVILSTDSQYVRQGITQWIHNWKARGWKTADKKPVKNVDLWQRLDAALGQHQ-IKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N + +E+AR AA
Sbjct: 119 EWVKGHAGHPENERCNELARAAA 141
>pdb|1JL1|A Chain A, D10a E. Coli Ribonuclease Hi
Length = 155
Score = 81.3 bits (199), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 52/143 (36%), Positives = 75/143 (52%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FT G+ N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 5 VEIFTAGSALGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALKE 61
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++ + + +W+ W+ GW+ AD KPV+N + Q L +GQ + +KW
Sbjct: 62 HA--EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-IKW 118
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
E+V GH N +ADE+AR AA
Sbjct: 119 EWVKGHAGHPENERADELARAAA 141
>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 = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 54/145 (37%), Positives = 76/145 (52%), Gaps = 7/145 (4%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDG+C N G Y G + AG R TNN E+ AI AL+ K
Sbjct: 4 QVEIFTDGSCLGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELMAAIVALEALK 60
Query: 66 SANIDRVCIKSDSQFMIKCV-QEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESV 124
V + +DSQ++ + + Q W+ W+ GW+ AD KPV+N + Q L +GQ + +
Sbjct: 61 EHC--EVILSTDSQYVRQGITQGWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQ-I 117
Query: 125 KWEFVPGHGNSHGNMKADEMARDAA 149
KWE+V GH N + DE+AR AA
Sbjct: 118 KWEWVKGHAGHPENERCDELARAAA 142
>pdb|1JL2|A Chain A, Crystal Structure Of Tceo Rnase H-A Chimera Combining The
Folding Core From T. Thermophilus Rnase H And The
Remaining Region Of E. Coli Rnase H
pdb|1JL2|B Chain B, Crystal Structure Of Tceo Rnase H-A Chimera Combining The
Folding Core From T. Thermophilus Rnase H And The
Remaining Region Of E. Coli Rnase H
pdb|1JL2|C Chain C, Crystal Structure Of Tceo Rnase H-A Chimera Combining The
Folding Core From T. Thermophilus Rnase H And The
Remaining Region Of E. Coli Rnase H
pdb|1JL2|D Chain D, Crystal Structure Of Tceo Rnase H-A Chimera Combining The
Folding Core From T. Thermophilus Rnase H And The
Remaining Region Of E. Coli Rnase H
Length = 156
Score = 79.7 bits (195), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 53/145 (36%), Positives = 75/145 (51%), Gaps = 9/145 (6%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
V +FTDG+ N G Y G + AG R TNN E++ AI LK K
Sbjct: 5 VEIFTDGSALGNPGPGGYGAILRYRGREKTFS-AGYT--RTTNNRMELKAAIEGLKALKE 61
Query: 67 -ANIDRVCIKSDSQFMIKCVQE-WMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESV 124
A +D + +DS ++ K E W+ W+ GWR A+GKPV+N++ + LL + V
Sbjct: 62 PAEVD---LYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP-HRV 117
Query: 125 KWEFVPGHGNSHGNMKADEMARDAA 149
++ FV GH N +ADE+AR AA
Sbjct: 118 RFHFVKGHAGHPENERADELARAAA 142
>pdb|1RIL|A Chain A, Crystal Structure Of Ribonuclease H From Thermus
Thermophilus Hb8 Refined At 2.8 Angstroms Resolution
Length = 166
Score = 73.9 bits (180), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 51/149 (34%), Positives = 72/149 (48%), Gaps = 7/149 (4%)
Query: 2 DPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHAL 61
P V +FTDGAC N G A + F + L G+ TNN E++ AI L
Sbjct: 4 SPRKRVALFTDGACLGNPGPGGWAAL-LRFHAHEKLLSGGEAC--TTNNRMELKAAIEGL 60
Query: 62 KQAKSANIDRVCIKSDSQFMIKCVQE-WMPKWQSNGWRKADGKPVQNKEELQELLHQIGQ 120
K K V + +DS ++ K E W+ W+ GWR A+GKPV+N++ + LL +
Sbjct: 61 KALKEPC--EVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAP 118
Query: 121 MESVKWEFVPGHGNSHGNMKADEMARDAA 149
V++ FV GH N + D AR A
Sbjct: 119 -HRVRFHFVKGHTGHPENERVDREARRQA 146
>pdb|3H08|A Chain A, Crystal Structure Of The Ribonuclease H1 From Chlorobium
Tepidum
pdb|3H08|B Chain B, Crystal Structure Of The Ribonuclease H1 From Chlorobium
Tepidum
Length = 146
Score = 73.9 bits (180), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 50/146 (34%), Positives = 76/146 (52%), Gaps = 13/146 (8%)
Query: 7 VVVFTDGAC---PRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
+ ++TDGA P G GA YG E + + A TNN E+ AI L+
Sbjct: 5 ITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPA------TTNNRMELMAAIKGLEA 58
Query: 64 AKSANIDRVCIKSDSQFMIKCVQE-WMPKWQSNGWRKADGKPVQNKEELQELLHQIGQME 122
K RV + SDS +++ + E W+ +W NGW+ A KPV+N + QE+L ++ +
Sbjct: 59 LKEP--ARVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEIL-KLTTLH 115
Query: 123 SVKWEFVPGHGNSHGNMKADEMARDA 148
V + V GH ++ N +ADE+AR A
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLA 141
>pdb|2ZQB|A Chain A, Crystal Structure Of A Psychrotrophic Rnasehi Variant With
Sextuple Thermostabilizing Mutations
pdb|2ZQB|B Chain B, Crystal Structure Of A Psychrotrophic Rnasehi Variant With
Sextuple Thermostabilizing Mutations
pdb|2ZQB|C Chain C, Crystal Structure Of A Psychrotrophic Rnasehi Variant With
Sextuple Thermostabilizing Mutations
pdb|2ZQB|D Chain D, Crystal Structure Of A Psychrotrophic Rnasehi Variant With
Sextuple Thermostabilizing Mutations
Length = 158
Score = 72.8 bits (177), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 46/146 (31%), Positives = 76/146 (52%), Gaps = 12/146 (8%)
Query: 7 VVVFTDGACPRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
+ +FTDG+C N G GYG+ Y G ++ +T TNN E+ I AL+
Sbjct: 7 IHIFTDGSCLGNPGPG---GYGIVMKYKGHTKEMSGGFSLT---TNNRMELLAPIVALEA 60
Query: 64 AKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMES 123
K ++ + SDSQ++ + + W+ W+ NGW ++G PV+N +L + L + Q+
Sbjct: 61 LKEPC--KIILTSDSQYVRQGIMTWIHGWKKNGWMTSNGTPVKNV-DLWKRLDKAAQLHQ 117
Query: 124 VKWEFVPGHGNSHGNMKADEMARDAA 149
+ W +V GH N + ++AR AA
Sbjct: 118 IDWRWVKGHAGHAENERCHQLARAAA 143
>pdb|2E4L|A Chain A, Thermodynamic And Structural Analysis Of Thermolabile
Rnase Hi From Shewanella Oneidensis Mr-1
Length = 158
Score = 72.4 bits (176), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 46/146 (31%), Positives = 75/146 (51%), Gaps = 12/146 (8%)
Query: 7 VVVFTDGACPRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
+ +FTDG+C N G GYG+ Y G ++ +T TNN E+ I AL+
Sbjct: 7 IHIFTDGSCLGNPGPG---GYGIVMNYKGHTKEMSDGFSLT---TNNRMELLAPIVALEA 60
Query: 64 AKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMES 123
K ++ + SDSQ+M + + W+ W+ GW ++ PV+N +L + L + Q+
Sbjct: 61 LKEPC--KIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNV-DLWKRLDKAAQLHQ 117
Query: 124 VKWEFVPGHGNSHGNMKADEMARDAA 149
+ W +V GH N + D++AR AA
Sbjct: 118 IDWRWVKGHAGHAENERCDQLARAAA 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 = 69.3 bits (168), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 40/136 (29%), Positives = 67/136 (49%), Gaps = 10/136 (7%)
Query: 10 FTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANI 69
+ DGA R K+G AGY G + + TN E+Q AL+ +
Sbjct: 16 YVDGAANRETKLG-KAGYVTNRGRQKVVTLTD-----TTNQKTELQAIYLALQDSGL--- 66
Query: 70 DRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWEFV 129
V I +DSQ+ + + +W+ W+ GW+ AD KPV+N + + +++ Q+ + E V +V
Sbjct: 67 -EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWV 125
Query: 130 PGHGNSHGNMKADEMA 145
P H GN + D++
Sbjct: 126 PAHKGIGGNEQVDKLV 141
>pdb|2RPI|A Chain A, The Nmr Structure Of The Submillisecond Folding
Intermediate Of The Thermus Thermophilus Ribonuclease H
Length = 112
Score = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 40/130 (30%), Positives = 58/130 (44%), Gaps = 30/130 (23%)
Query: 2 DPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHAL 61
P V +FTDGA N G TNN E++ AI L
Sbjct: 4 SPRKRVALFTDGAALGNPGPG------------------------TTNNRMELKAAIEGL 39
Query: 62 KQAKS-ANIDRVCIKSDSQFMIKCVQE-WMPKWQSNGWRKADGKPVQNKEELQELLHQIG 119
K K A +D + +DS ++ K E W+ W+ GWR A+GKPV+N++ + LL +
Sbjct: 40 KALKEPAEVD---LYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA 96
Query: 120 QMESVKWEFV 129
V++ FV
Sbjct: 97 P-HRVRFHFV 105
>pdb|4E89|A Chain A, Crystal Structure Of Rnaseh From Gammaretrovirus
Length = 157
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 8/108 (7%)
Query: 47 VTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQ 106
+ AE+ ALK A+ ++ + +DS++ ++ G ++G+ ++
Sbjct: 50 TSAQRAELIALTQALKMAEGKKLN---VYTDSRYAFATAHVHGEIYRRRGLLTSEGREIK 106
Query: 107 NKEELQELLHQIGQMESVKWEFVPGH--GNS---HGNMKADEMARDAA 149
NK E+ LL + + + PGH GNS GN AD+ AR+AA
Sbjct: 107 NKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA 154
>pdb|3V1O|A Chain A, Crystal Structures Of The Reverse Transcriptase-Associated
Ribonuclease H Domain Of Xenotropic Murine
Leukemia-Virus Related Virus
pdb|3V1R|A Chain A, Crystal Structures Of The Reverse Transcriptase-Associated
Ribonuclease H Domain Of Xmrv With Inhibitor
Beta-Thujaplicinol
Length = 180
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 8/108 (7%)
Query: 47 VTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQ 106
+ AE+ ALK A+ ++ + +DS++ ++ G ++G+ ++
Sbjct: 65 TSAQRAELIALTQALKMAEGKKLN---VYTDSRYAFATAHVHGEIYRRRGLLTSEGREIK 121
Query: 107 NKEELQELLHQIGQMESVKWEFVPGH--GNS---HGNMKADEMARDAA 149
NK E+ LL + + + PGH GNS GN AD+ AR+AA
Sbjct: 122 NKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA 169
>pdb|4HKQ|A Chain A, Protein Dna Complex
Length = 681
Score = 37.4 bits (85), Expect = 0.003, Method: Composition-based stats.
Identities = 28/103 (27%), Positives = 50/103 (48%), Gaps = 8/103 (7%)
Query: 52 AEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEEL 111
AE+ ALK A+ ++ + ++S++ ++ G ++G+ ++NK E+
Sbjct: 571 AELIALTQALKMAEGKKLN---VYTNSRYAFATAHVHGEIYRRRGLLTSEGREIKNKNEI 627
Query: 112 QELLHQIGQMESVKWEFVPGH--GNS---HGNMKADEMARDAA 149
LL + + + PGH GNS GN AD+ AR+AA
Sbjct: 628 LALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA 670
>pdb|2LSN|A Chain A, Solution Structure Of Pfv Rnase H Domain
Length = 165
Score = 35.0 bits (79), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 36/150 (24%), Positives = 64/150 (42%), Gaps = 13/150 (8%)
Query: 8 VVFTDGACPRNGKVGAS--AGYGVYFGENNP----LNVAGKVTGRVTNNNAEIQGAIHAL 61
V +TDG+ ++ S AG G+ P LN G T AEI A
Sbjct: 9 VFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFAC 68
Query: 62 KQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQM 121
K+A V + +DS ++ + + +P W+SNG+ KP+++ + + + +
Sbjct: 69 KKALKIP-GPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMK 127
Query: 122 ESVKWEFVPGHG------NSHGNMKADEMA 145
+ + GH ++ GN AD++A
Sbjct: 128 PDITIQHEKGHQPTNTSIHTEGNALADKLA 157
>pdb|1BQN|A Chain A, Tyr 188 Leu Hiv-1 RtHBY 097
Length = 558
Score = 33.9 bits (76), Expect = 0.034, Method: Composition-based stats.
Identities = 34/136 (25%), Positives = 58/136 (42%), Gaps = 26/136 (19%)
Query: 10 FTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANI 69
+ DGA R K+G AGY G + + TN E+Q AL+ +
Sbjct: 441 YVDGAANRETKLG-KAGYVTNKGRQKVVPLTN-----TTNQKTELQAIYLALQDSGL--- 491
Query: 70 DRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEEL-QELLHQIGQMESVKWEF 128
V I +DSQ+ + +Q +P +++ EL +++ Q+ + E V +
Sbjct: 492 -EVNIVTDSQYALGIIQ---------------AQPDKSESELVNQIIEQLIKKEKVYLAW 535
Query: 129 VPGHGNSHGNMKADEM 144
VP H GN + D++
Sbjct: 536 VPAHKGIGGNQQVDKL 551
>pdb|2HB5|A Chain A, Crystal Structure Of The Moloney Murine Leukemia Virus
Rnase H Domain
Length = 164
Score = 33.9 bits (76), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 19/108 (17%)
Query: 47 VTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQ 106
+ AE+ ALK A+ ++ + +DS++ + ++GK ++
Sbjct: 60 TSAQRAELIALTQALKXAEGKKLN---VYTDSRYAF-----------ATAHLTSEGKEIK 105
Query: 107 NKEELQELLHQIGQMESVKWEFVPGHGNSH-----GNMKADEMARDAA 149
NK+E+ LL + + + PGH H GN AD+ AR AA
Sbjct: 106 NKDEILALLKALFLPKRLSIIHCPGHQKGHSAEARGNRXADQAARKAA 153
>pdb|1MU2|A Chain A, Crystal Structure Of Hiv-2 Reverse Transcriptase
Length = 555
Score = 33.1 bits (74), Expect = 0.062, Method: Composition-based stats.
Identities = 32/136 (23%), Positives = 61/136 (44%), Gaps = 26/136 (19%)
Query: 10 FTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANI 69
+TDG+C R K G AGY G++ K + TN AE++ AL +
Sbjct: 440 YTDGSCNRQSKEG-KAGYVTDRGKDKV-----KKLEQTTNQQAELEAFAMALTDSGP--- 490
Query: 70 DRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEEL-QELLHQIGQMESVKWEF 128
+V I DSQ+++ V +P +++ ++ +++ ++ + E++ +
Sbjct: 491 -KVNIIVDSQYVMGIVAS---------------QPTESESKIVNQIIEEMIKKEAIYVAW 534
Query: 129 VPGHGNSHGNMKADEM 144
VP H GN + D +
Sbjct: 535 VPAHKGIGGNQEVDHL 550
>pdb|3V1Q|A Chain A, Crystal Structures Of The Reverse Transcriptase-Associated
Ribonuclease H Domain Of Xenotropic Murine
Leukemia-Virus Related Virus
Length = 167
Score = 32.3 bits (72), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 49/108 (45%), Gaps = 19/108 (17%)
Query: 47 VTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQ 106
+ AE+ ALK A+ ++ + +DS++ + ++G+ ++
Sbjct: 63 TSAQRAELIALTQALKMAEGKKLN---VYTDSRYAF-----------ATAHVHSEGREIK 108
Query: 107 NKEELQELLHQIGQMESVKWEFVPGH--GNS---HGNMKADEMARDAA 149
NK E+ LL + + + PGH GNS GN AD+ AR+AA
Sbjct: 109 NKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA 156
>pdb|3P1G|A Chain A, Crystal Structure Of The Xenotropic Murine Leukemia
Virus-Related Virus (Xmrv) Rnase H Domain
Length = 165
Score = 32.3 bits (72), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 49/108 (45%), Gaps = 19/108 (17%)
Query: 47 VTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQ 106
+ AE+ ALK A+ ++ + +DS++ + ++G+ ++
Sbjct: 61 TSAQRAELIALTQALKMAEGKKLN---VYTDSRYAF-----------ATAHVHSEGREIK 106
Query: 107 NKEELQELLHQIGQMESVKWEFVPGH--GNS---HGNMKADEMARDAA 149
NK E+ LL + + + PGH GNS GN AD+ AR+AA
Sbjct: 107 NKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAA 154
>pdb|3ALY|A Chain A, Crystal Structure Of Rnase Hi From Sulfolobus Tokodaii
With C-Terminal Deletion
pdb|3ALY|B Chain B, Crystal Structure Of Rnase Hi From Sulfolobus Tokodaii
With C-Terminal Deletion
Length = 143
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 44/104 (42%), Gaps = 15/104 (14%)
Query: 7 VVVFTDGAC-PRNGKVGASAGYGVYFGENNPLNVAG----KVTGRVTNNNAEIQGAIHAL 61
++ + DG C P+N A+ G+ +Y +N + G + TNN AE G I +
Sbjct: 2 IIGYFDGLCEPKNPGGIATFGFVIYL-DNRKIEGYGLAEKPFSINSTNNVAEYSGLICLM 60
Query: 62 KQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPV 105
+ I IK DSQ +IK Q NG K K +
Sbjct: 61 ETMLRLGISSPIIKGDSQLVIK---------QMNGEYKVKAKRI 95
>pdb|2EHG|A Chain A, Crystal Structure Of Hyperthermophilic Archaeal Rnase Hi
Length = 149
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 44/104 (42%), Gaps = 15/104 (14%)
Query: 7 VVVFTDGAC-PRNGKVGASAGYGVYFGENNPLNVAG----KVTGRVTNNNAEIQGAIHAL 61
++ + DG C P+N A+ G+ +Y +N + G + TNN AE G I +
Sbjct: 2 IIGYFDGLCEPKNPGGIATFGFVIYL-DNRKIEGYGLAEKPFSINSTNNVAEYSGLICLM 60
Query: 62 KQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPV 105
+ I IK DSQ +IK Q NG K K +
Sbjct: 61 ETMLRLGISSPIIKGDSQLVIK---------QMNGEYKVKAKRI 95
>pdb|1ZBL|A Chain A, Bacillus Halodurans Rnase H Catalytic Domain Mutant D192n
In Complex With 12-Mer RnaDNA HYBRID
pdb|1ZBL|B Chain B, Bacillus Halodurans Rnase H Catalytic Domain Mutant D192n
In Complex With 12-Mer RnaDNA HYBRID
Length = 139
Score = 30.4 bits (67), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 22 GASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFM 81
G G E P+ + TNN E +H L+ K N R I SDSQ
Sbjct: 31 GVDTKTGEVLFEREPIPIG-------TNNMGEFLAIVHGLRYLKERN-SRKPIYSDSQTA 82
Query: 82 IKCVQEWMPKWQSNGWRKADGKPVQNKE 109
IK V++ +KA V+N+E
Sbjct: 83 IKWVKD----------KKAKSTLVRNEE 100
>pdb|2G8F|A Chain A, B. Halodurans Rnase H Catalytic Domain E188a Mutant In
Complex With Mg2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
pdb|2G8V|A Chain A, B. Halodurans Rnase H Catalytic Domain E188a Mutant In
Complex With Mg2+ And Rna/dna Hybrid (reaction Product)
pdb|2G8W|A Chain A, B. Halodurans Rnase H Catalytic Domain E188a Mutant In
Complex With Ca2+ And RnaDNA HYBRID
Length = 142
Score = 30.0 bits (66), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 22 GASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFM 81
G G E P+ + TNN E +H L+ K N R I SDSQ
Sbjct: 31 GVDTKTGEVLFEREPIPIG-------TNNMGEFLAIVHGLRYLKERN-SRKPIYSDSQTA 82
Query: 82 IKCVQEWMPKWQSNGWRKADGKPVQNKE 109
IK V++ +KA V+N+E
Sbjct: 83 IKWVKD----------KKAKSTLVRNEE 100
>pdb|3HST|B Chain B, N-Terminal Rnase H Domain Of Rv2228c From Mycobacterium
Tuberculosis As A Fusion Protein With Maltose Binding
Protein
pdb|3HST|D Chain D, N-Terminal Rnase H Domain Of Rv2228c From Mycobacterium
Tuberculosis As A Fusion Protein With Maltose Binding
Protein
Length = 141
Score = 30.0 bits (66), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 33/139 (23%), Positives = 55/139 (39%), Gaps = 17/139 (12%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYF---GENNPLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
VV+ DG N AGYG + L + + GR TNN AE +G I L
Sbjct: 4 VVIEADGGSRGNP---GPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDD 60
Query: 64 AKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMES 123
A + DS+ +++ + S W+ ++ + Q L Q
Sbjct: 61 AVKLGATEAAVLMDSKLVVEQM--------SGRWKVKHPDLLKLYVQAQAL---ASQFRR 109
Query: 124 VKWEFVPGHGNSHGNMKAD 142
+ +E+VP N++ + A+
Sbjct: 110 INYEWVPRARNTYADRLAN 128
>pdb|2G8H|A Chain A, B. Halodurans Rnase H Catalytic Domain D192n Mutant In
Complex With Mg2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
pdb|2G8I|A Chain A, B. Halodurans Rnase H Catalytic Domain D192n Mutant In
Complex With Mn2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
pdb|2G8K|A Chain A, B. Halodurans Rnase H Catalytic Domain D192n Mutant In
Complex With Ca2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
Length = 142
Score = 30.0 bits (66), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 22 GASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFM 81
G G E P+ + TNN E +H L+ K N R I SDSQ
Sbjct: 31 GVDTKTGEVLFEREPIPIG-------TNNMGEFLAIVHGLRYLKERN-SRKPIYSDSQTA 82
Query: 82 IKCVQEWMPKWQSNGWRKADGKPVQNKE 109
IK V++ +KA V+N+E
Sbjct: 83 IKWVKD----------KKAKSTLVRNEE 100
>pdb|3D9W|A Chain A, Crystal Structure Analysis Of Nocardia Farcinica Arylamine
N-Acetyltransferase
pdb|3D9W|B Chain B, Crystal Structure Analysis Of Nocardia Farcinica Arylamine
N-Acetyltransferase
pdb|3D9W|C Chain C, Crystal Structure Analysis Of Nocardia Farcinica Arylamine
N-Acetyltransferase
pdb|3D9W|D Chain D, Crystal Structure Analysis Of Nocardia Farcinica Arylamine
N-Acetyltransferase
Length = 293
Score = 29.3 bits (64), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 13 GACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRV 72
G C N + A+A + FG V G TGRVT ++ A HAL + +A+ DRV
Sbjct: 80 GYCYENAGLFAAALERLGFG------VTGH-TGRVTMGAGGLRPATHALLRVTTADDDRV 132
>pdb|3D0P|A Chain A, Insights Into RnaDNA HYBRID RECOGNITION AND PROCESSING BY
Rnase H From The Crystal Structure Of A Non-Specific
Enzyme-Dsdna Complex
pdb|3D0P|C Chain C, Insights Into RnaDNA HYBRID RECOGNITION AND PROCESSING BY
Rnase H From The Crystal Structure Of A Non-Specific
Enzyme-Dsdna Complex
pdb|4HTU|A Chain A, Structure Of 5-chlorouracil Modified A:u Base Pair
pdb|4HTU|B Chain B, Structure Of 5-chlorouracil Modified A:u Base Pair
pdb|4HUE|A Chain A, Structure Of 5-chlorouracil Modified G:u Base Pair
pdb|4HUE|B Chain B, Structure Of 5-chlorouracil Modified G:u Base Pair
pdb|4HUF|A Chain A, Structure Of 5-chlorouracil Modified A:u Base Pair
pdb|4HUF|B Chain B, Structure Of 5-chlorouracil Modified A:u Base Pair
pdb|4HUG|A Chain A, Structure Of 5-chlorouracil Modified A:u Base Pairs
pdb|4HUG|B Chain B, Structure Of 5-chlorouracil Modified A:u Base Pairs
Length = 134
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 22 GASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFM 81
G G E P+ + TNN E +H L+ K N R I S+SQ
Sbjct: 25 GVDTKTGEVLFEREPIPIG-------TNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTA 76
Query: 82 IKCVQEWMPKWQSNGWRKADGKPVQNKE 109
IK V++ +KA V+N+E
Sbjct: 77 IKWVKD----------KKAKSTLVRNEE 94
>pdb|1ZBF|A Chain A, Crystal Structure Of B. Halodurans Rnase H Catalytic
Domain Mutant D132n
pdb|1ZBI|A Chain A, Bacillus Halodurans Rnase H Catalytic Domain Mutant D132n
In Complex With 12-Mer RnaDNA HYBRID
pdb|1ZBI|B Chain B, Bacillus Halodurans Rnase H Catalytic Domain Mutant D132n
In Complex With 12-Mer RnaDNA HYBRID
pdb|2G8U|A Chain A, B. Halodurans Rnase H Catalytic Domain D132n Mutant In
Complex With Mg2+ And RnaDNA HYBRID (NON-P Nick At The
Active Site)
pdb|3ULD|A Chain A, High Resolution Structure Of DnaRNA HYBRID IN COMPLEX WITH
RNASE H Catalytic Domain D132n Mutant
Length = 142
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 22 GASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFM 81
G G E P+ + TNN E +H L+ K N R I S+SQ
Sbjct: 31 GVDTKTGEVLFEREPIPIG-------TNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTA 82
Query: 82 IKCVQEWMPKWQSNGWRKADGKPVQNKE 109
IK V++ +KA V+N+E
Sbjct: 83 IKWVKD----------KKAKSTLVRNEE 100
>pdb|2R7Y|A Chain A, Selenium Derivatized RnaDNA HYBRID IN COMPLEX WITH RNASE H
Catalytic Domain Mutant D132n
pdb|3I8D|A Chain A, The Pairing Geometry Of The Hydrophobic Thymine Analog
2,4- Difluorotoluene In Duplex Dna As Analyzed By X-Ray
Crystallography
pdb|3I8D|C Chain C, The Pairing Geometry Of The Hydrophobic Thymine Analog
2,4- Difluorotoluene In Duplex Dna As Analyzed By X-Ray
Crystallography
Length = 132
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 22 GASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFM 81
G G E P+ + TNN E +H L+ K N R I S+SQ
Sbjct: 24 GVDTKTGEVLFEREPIPIG-------TNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTA 75
Query: 82 IKCVQEWMPKWQSNGWRKADGKPVQNKE 109
IK V++ +KA V+N+E
Sbjct: 76 IKWVKD----------KKAKSTLVRNEE 93
>pdb|3EY1|A Chain A, A Conformational Transition In The Structure Of A
2'-Thiomethyl- Modified Dna Visualized At High
Resolution
pdb|3TWH|A Chain A, Selenium Derivatized RnaDNA HYBRID IN COMPLEX WITH RNASE H
CATALYTIC Domain D132n Mutant
Length = 138
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 22 GASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFM 81
G G E P+ + TNN E +H L+ K N R I S+SQ
Sbjct: 27 GVDTKTGEVLFEREPIPIG-------TNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTA 78
Query: 82 IKCVQEWMPKWQSNGWRKADGKPVQNKE 109
IK V++ +KA V+N+E
Sbjct: 79 IKWVKD----------KKAKSTLVRNEE 96
>pdb|1X0U|A Chain A, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|B Chain B, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|C Chain C, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|D Chain D, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|E Chain E, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|F Chain F, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
Length = 522
Score = 26.6 bits (57), Expect = 5.4, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 17/35 (48%)
Query: 39 VAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVC 73
+AG V G V NN E G+I K+A R C
Sbjct: 322 IAGNVVGIVANNPEEFGGSIDIDAADKAARFIRFC 356
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
0.315 0.131 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,231,116
Number of Sequences: 62578
Number of extensions: 207440
Number of successful extensions: 455
Number of sequences better than 100.0: 69
Number of HSP's better than 100.0 without gapping: 54
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 357
Number of HSP's gapped (non-prelim): 69
length of query: 151
length of database: 14,973,337
effective HSP length: 90
effective length of query: 61
effective length of database: 9,341,317
effective search space: 569820337
effective search space used: 569820337
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 47 (22.7 bits)