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= 003687
(803 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NNE|A Chain A, Crystal Structure Of The Muts-adpbef3-dna Complex
pdb|1NNE|B Chain B, Crystal Structure Of The Muts-adpbef3-dna Complex
Length = 765
Score = 112 bits (281), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 73/204 (35%), Positives = 102/204 (50%), Gaps = 11/204 (5%)
Query: 496 VHNTVDM-QSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMK 554
V N ++M L L+TGPN GKS+ LR +LL G VPAE A +P FD I +
Sbjct: 568 VPNDLEMAHELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIG 627
Query: 555 SYDSPADGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDNI 614
+ D A GKS+F VEM E+ I+ T SLVL+DE+ RGT + G IA ++ E L
Sbjct: 628 ASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEALHER 687
Query: 615 GCLGIVSTHLHGIFSLPL-KIKN---AAYKAMGTEYLDGQTVPTWKLVDGICRESLAFET 670
+ +TH + +L L ++KN AA + G Q +P G +S E
Sbjct: 688 RAYTLFATHYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLP------GPASKSYGVEV 741
Query: 671 AKREGVPETIIQRAEDLYIACGVN 694
A G+P+ ++ RA L A
Sbjct: 742 AAMAGLPKEVVARARALLQAMAAR 765
>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|B Chain B, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8E|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
pdb|2O8F|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
Length = 1022
Score = 105 bits (261), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 62/186 (33%), Positives = 99/186 (53%), Gaps = 8/186 (4%)
Query: 507 LLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYDSPADGKSSF 566
L+TGPN GGKS+L+R +++ G VPAE + D + + + D G+S+F
Sbjct: 793 LVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTF 852
Query: 567 QVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETL-DNIGCLGIVSTHLH 625
VE+SE SI+ T+ SLVL+DE+ RGT T GT IA ++++ L + I C + STH H
Sbjct: 853 FVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYH 912
Query: 626 GI---FSLPLKIKNAAYKAMGTEYLDGQTVPT----WKLVDGICRESLAFETAKREGVPE 678
+ +S + ++ M + + T +K + G C +S F A+ +PE
Sbjct: 913 SLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPE 972
Query: 679 TIIQRA 684
+IQ+
Sbjct: 973 EVIQKG 978
>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts
pdb|1EWR|B Chain B, Crystal Structure Of Taq Muts
Length = 649
Score = 104 bits (260), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 92/183 (50%), Gaps = 10/183 (5%)
Query: 503 QSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYDSPADG 562
L L+TGPN GKS+ LR +LL G VPAE A +P FD I + + D A G
Sbjct: 460 HELVLITGPNXAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGG 519
Query: 563 KSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDNIGCLGIVST 622
KS+F VE E+ I+ T SLVL+DE+ RGT + G IA ++ E L + +T
Sbjct: 520 KSTFXVEXEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEALHERRAYTLFAT 579
Query: 623 HLHGIFSLPL-KIKN---AAYKAMGTEYLDGQTVPTWKLVDGICRESLAFETAKREGVPE 678
H + +L L ++KN AA + G Q +P G +S E A G+P+
Sbjct: 580 HYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLP------GPASKSYGVEVAAXAGLPK 633
Query: 679 TII 681
++
Sbjct: 634 EVV 636
>pdb|1FW6|A Chain A, Crystal Structure Of A Taq Muts-Dna-Adp Ternary Complex
pdb|1FW6|B Chain B, Crystal Structure Of A Taq Muts-Dna-Adp Ternary Complex
Length = 768
Score = 104 bits (260), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 92/183 (50%), Gaps = 10/183 (5%)
Query: 503 QSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYDSPADG 562
L L+TGPN GKS+ LR +LL G VPAE A +P FD I + + D A G
Sbjct: 576 HELVLITGPNXAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGG 635
Query: 563 KSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDNIGCLGIVST 622
KS+F VE E+ I+ T SLVL+DE+ RGT + G IA ++ E L + +T
Sbjct: 636 KSTFXVEXEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEALHERRAYTLFAT 695
Query: 623 HLHGIFSLPL-KIKN---AAYKAMGTEYLDGQTVPTWKLVDGICRESLAFETAKREGVPE 678
H + +L L ++KN AA + G Q +P G +S E A G+P+
Sbjct: 696 HYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLP------GPASKSYGVEVAAXAGLPK 749
Query: 679 TII 681
++
Sbjct: 750 EVV 752
>pdb|1EWQ|A Chain A, Crystal Structure Taq Muts Complexed With A Heteroduplex
Dna At 2.2 A Resolution
pdb|1EWQ|B Chain B, Crystal Structure Taq Muts Complexed With A Heteroduplex
Dna At 2.2 A Resolution
Length = 765
Score = 104 bits (260), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 65/183 (35%), Positives = 92/183 (50%), Gaps = 10/183 (5%)
Query: 503 QSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYDSPADG 562
L L+TGPN GKS+ LR +LL G VPAE A +P FD I + + D A G
Sbjct: 576 HELVLITGPNXAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGG 635
Query: 563 KSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDNIGCLGIVST 622
KS+F VE E+ I+ T SLVL+DE+ RGT + G IA ++ E L + +T
Sbjct: 636 KSTFXVEXEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEALHERRAYTLFAT 695
Query: 623 HLHGIFSLPL-KIKN---AAYKAMGTEYLDGQTVPTWKLVDGICRESLAFETAKREGVPE 678
H + +L L ++KN AA + G Q +P G +S E A G+P+
Sbjct: 696 HYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLP------GPASKSYGVEVAAXAGLPK 749
Query: 679 TII 681
++
Sbjct: 750 EVV 752
>pdb|1OH5|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With
A C:a Mismatch
pdb|1OH5|B Chain B, The Crystal Structure Of E. Coli Muts Binding To Dna With
A C:a Mismatch
pdb|1OH6|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With
An A:a Mismatch
pdb|1OH6|B Chain B, The Crystal Structure Of E. Coli Muts Binding To Dna With
An A:a Mismatch
pdb|1OH7|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With
A G:g Mismatch
pdb|1OH7|B Chain B, The Crystal Structure Of E. Coli Muts Binding To Dna With
A G:g Mismatch
pdb|1OH8|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With
An Unpaired Thymidine
pdb|1OH8|B Chain B, The Crystal Structure Of E. Coli Muts Binding To Dna With
An Unpaired Thymidine
pdb|1W7A|A Chain A, Atp Bound Muts
pdb|1W7A|B Chain B, Atp Bound Muts
pdb|2WTU|A Chain A, Crystal Structure Of Escherichia Coli Muts In Complex With
A 16 Basepair Oligo Containing An A.A Mismatch.
pdb|2WTU|B Chain B, Crystal Structure Of Escherichia Coli Muts In Complex With
A 16 Basepair Oligo Containing An A.A Mismatch
Length = 800
Score = 103 bits (256), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 68/193 (35%), Positives = 98/193 (50%), Gaps = 11/193 (5%)
Query: 498 NTVDMQSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYD 557
N + + ++TGPN GGKS+ +R +L+ G VPA+ I D I + + D
Sbjct: 602 NLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAAD 661
Query: 558 SPADGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDN-IGC 616
A G+S+F VEM+E +I+ T SLVL+DEI RGT T G +A + E L N I
Sbjct: 662 DLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKA 721
Query: 617 LGIVSTHLHGIFSLPLKIKNAAYKAMGTEYLD----GQTVPTWKLV-DGICRESLAFETA 671
L + +TH + LP K++ A +LD G T+ V DG +S A
Sbjct: 722 LTLFATHYFELTQLPEKMEGVA-----NVHLDALEHGDTIAFMHSVQDGAASKSYGLAVA 776
Query: 672 KREGVPETIIQRA 684
GVP+ +I+RA
Sbjct: 777 ALAGVPKEVIKRA 789
>pdb|1WBD|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme
Muts, E38q Mutant, In Complex With A G.T Mismatch
pdb|1WBD|B Chain B, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme
Muts, E38q Mutant, In Complex With A G.T Mismatch
Length = 800
Score = 103 bits (256), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 68/193 (35%), Positives = 98/193 (50%), Gaps = 11/193 (5%)
Query: 498 NTVDMQSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYD 557
N + + ++TGPN GGKS+ +R +L+ G VPA+ I D I + + D
Sbjct: 602 NLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAAD 661
Query: 558 SPADGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDN-IGC 616
A G+S+F VEM+E +I+ T SLVL+DEI RGT T G +A + E L N I
Sbjct: 662 DLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKA 721
Query: 617 LGIVSTHLHGIFSLPLKIKNAAYKAMGTEYLD----GQTVPTWKLV-DGICRESLAFETA 671
L + +TH + LP K++ A +LD G T+ V DG +S A
Sbjct: 722 LTLFATHYFELTQLPEKMEGVA-----NVHLDALEHGDTIAFMHSVQDGAASKSYGLAVA 776
Query: 672 KREGVPETIIQRA 684
GVP+ +I+RA
Sbjct: 777 ALAGVPKEVIKRA 789
>pdb|1WBB|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme
Muts, E38a Mutant, In Complex With A G.T Mismatch
pdb|1WBB|B Chain B, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme
Muts, E38a Mutant, In Complex With A G.T Mismatch
Length = 800
Score = 102 bits (255), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 68/193 (35%), Positives = 98/193 (50%), Gaps = 11/193 (5%)
Query: 498 NTVDMQSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYD 557
N + + ++TGPN GGKS+ +R +L+ G VPA+ I D I + + D
Sbjct: 602 NLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAAD 661
Query: 558 SPADGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDN-IGC 616
A G+S+F VEM+E +I+ T SLVL+DEI RGT T G +A + E L N I
Sbjct: 662 DLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKA 721
Query: 617 LGIVSTHLHGIFSLPLKIKNAAYKAMGTEYLD----GQTVPTWKLV-DGICRESLAFETA 671
L + +TH + LP K++ A +LD G T+ V DG +S A
Sbjct: 722 LTLFATHYFELTQLPEKMEGVA-----NVHLDALEHGDTIAFMHSVQDGAASKSYGLAVA 776
Query: 672 KREGVPETIIQRA 684
GVP+ +I+RA
Sbjct: 777 ALAGVPKEVIKRA 789
>pdb|1WB9|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme
Muts, E38t Mutant, In Complex With A G.T Mismatch
pdb|1WB9|B Chain B, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme
Muts, E38t Mutant, In Complex With A G.T Mismatch
Length = 800
Score = 102 bits (255), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 68/193 (35%), Positives = 98/193 (50%), Gaps = 11/193 (5%)
Query: 498 NTVDMQSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYD 557
N + + ++TGPN GGKS+ +R +L+ G VPA+ I D I + + D
Sbjct: 602 NLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAAD 661
Query: 558 SPADGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDN-IGC 616
A G+S+F VEM+E +I+ T SLVL+DEI RGT T G +A + E L N I
Sbjct: 662 DLASGRSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKA 721
Query: 617 LGIVSTHLHGIFSLPLKIKNAAYKAMGTEYLD----GQTVPTWKLV-DGICRESLAFETA 671
L + +TH + LP K++ A +LD G T+ V DG +S A
Sbjct: 722 LTLFATHYFELTQLPEKMEGVA-----NVHLDALEHGDTIAFMHSVQDGAASKSYGLAVA 776
Query: 672 KREGVPETIIQRA 684
GVP+ +I+RA
Sbjct: 777 ALAGVPKEVIKRA 789
>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
pdb|2O8C|A Chain A, Human Mutsalpha (msh2/msh6) Bound To Adp And An
O6-methyl-guanine T Mispair
pdb|2O8D|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
pdb|2O8F|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE
T INSERT
pdb|3THW|A Chain A, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|A Chain A, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|A Chain A, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|A Chain A, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 934
Score = 102 bits (253), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 88/328 (26%), Positives = 145/328 (44%), Gaps = 31/328 (9%)
Query: 408 YHEAGAKAKAKVLELLRGLSSELQTKINILVFASMLLVIGKALFAHVSEGRRRKWVFPAL 467
Y EA +++ + G +QT ++L A + V+ FAHVS G +V PA+
Sbjct: 570 YEEAQDAIVKEIVNISSGYVEPMQTLNDVL--AQLDAVVS---FAHVSNGAPVPYVRPAI 624
Query: 468 KD-------IELDGANCLKMNGLSPYWFDAAEGSAVHNTVDMQSLFLLTGPNGGGKSSLL 520
+ ++ C+++ + + V+ D Q ++TGPN GGKS+ +
Sbjct: 625 LEKGQGRIILKASRHACVEVQDEIAFI-----PNDVYFEKDKQMFHIITGPNMGGKSTYI 679
Query: 521 RSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYDSPADGKSSFQVEMSEIRSIVTAT 580
R L+ G VP ESA + D I+ + + DS G S+F EM E SI+ +
Sbjct: 680 RQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSA 739
Query: 581 TSRSLVLIDEICRGTETAKGTCIAGSIIETL-DNIGCLGIVSTHLHGIFSLPLKIKNAAY 639
T SL++IDE+ RGT T G +A +I E + IG + +TH H + +L +I
Sbjct: 740 TKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTVNN 799
Query: 640 KAMGTEYLDGQTVPTWKLVDGICRESLAFETAKREGVPETIIQRAEDLYIACGVNCVMIA 699
+ + +++ G+C +S A+ P+ +I+ C
Sbjct: 800 LHVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIE------------CAKQK 847
Query: 700 AREQPPPSIIGASCVYVMLRP-DKKLYI 726
A E IG S Y ++ P KK Y+
Sbjct: 848 ALELEEFQYIGESQGYDIMEPAAKKCYL 875
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 102 bits (253), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 88/328 (26%), Positives = 145/328 (44%), Gaps = 31/328 (9%)
Query: 408 YHEAGAKAKAKVLELLRGLSSELQTKINILVFASMLLVIGKALFAHVSEGRRRKWVFPAL 467
Y EA +++ + G +QT ++L A + V+ FAHVS G +V PA+
Sbjct: 570 YEEAQDAIVKEIVNISSGYVEPMQTLNDVL--AQLDAVVS---FAHVSNGAPVPYVRPAI 624
Query: 468 KD-------IELDGANCLKMNGLSPYWFDAAEGSAVHNTVDMQSLFLLTGPNGGGKSSLL 520
+ ++ C+++ + + V+ D Q ++TGPN GGKS+ +
Sbjct: 625 LEKGQGRIILKASRHACVEVQDEIAFI-----PNDVYFEKDKQMFHIITGPNMGGKSTYI 679
Query: 521 RSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYDSPADGKSSFQVEMSEIRSIVTAT 580
R L+ G VP ESA + D I+ + + DS G S+F EM E SI+ +
Sbjct: 680 RQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSA 739
Query: 581 TSRSLVLIDEICRGTETAKGTCIAGSIIETL-DNIGCLGIVSTHLHGIFSLPLKIKNAAY 639
T SL++IDE+ RGT T G +A +I E + IG + +TH H + +L +I
Sbjct: 740 TKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTVNN 799
Query: 640 KAMGTEYLDGQTVPTWKLVDGICRESLAFETAKREGVPETIIQRAEDLYIACGVNCVMIA 699
+ + +++ G+C +S A+ P+ +I+ C
Sbjct: 800 LHVTALTTEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIE------------CAKQK 847
Query: 700 AREQPPPSIIGASCVYVMLRP-DKKLYI 726
A E IG S Y ++ P KK Y+
Sbjct: 848 ALELEEFQYIGESQGYDIMEPAAKKCYL 875
>pdb|3K0S|A Chain A, Crystal Structure Of E.Coli Dna Mismatch Repair Protein
Muts, D693n Mutant, In Complex With Gt Mismatched Dna
pdb|3K0S|B Chain B, Crystal Structure Of E.Coli Dna Mismatch Repair Protein
Muts, D693n Mutant, In Complex With Gt Mismatched Dna
Length = 799
Score = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 67/193 (34%), Positives = 98/193 (50%), Gaps = 11/193 (5%)
Query: 498 NTVDMQSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYD 557
N + + ++TGPN GGKS+ +R +L+ G VPA+ I D I + + D
Sbjct: 601 NLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAAD 660
Query: 558 SPADGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDN-IGC 616
A G+S+F VEM+E +I+ T SLVL++EI RGT T G +A + E L N I
Sbjct: 661 DLASGRSTFMVEMTETANILHNATEYSLVLMNEIGRGTSTYDGLSLAWACAENLANKIKA 720
Query: 617 LGIVSTHLHGIFSLPLKIKNAAYKAMGTEYLD----GQTVPTWKLV-DGICRESLAFETA 671
L + +TH + LP K++ A +LD G T+ V DG +S A
Sbjct: 721 LTLFATHYFELTQLPEKMEGVA-----NVHLDALEHGDTIAFMHSVQDGAASKSYGLAVA 775
Query: 672 KREGVPETIIQRA 684
GVP+ +I+RA
Sbjct: 776 ALAGVPKEVIKRA 788
>pdb|1NG9|A Chain A, E.Coli Muts R697a: An Atpase-Asymmetry Mutant
pdb|1NG9|B Chain B, E.Coli Muts R697a: An Atpase-Asymmetry Mutant
Length = 800
Score = 100 bits (248), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 67/193 (34%), Positives = 97/193 (50%), Gaps = 11/193 (5%)
Query: 498 NTVDMQSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYD 557
N + + ++TGPN GGKS+ +R +L+ G VPA+ I D I + + D
Sbjct: 602 NLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAAD 661
Query: 558 SPADGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDN-IGC 616
A G+S+F VEM+E +I+ T SLVL+DEI GT T G +A + E L N I
Sbjct: 662 DLASGRSTFMVEMTETANILHNATEYSLVLMDEIGAGTSTYDGLSLAWACAENLANKIKA 721
Query: 617 LGIVSTHLHGIFSLPLKIKNAAYKAMGTEYLD----GQTVPTWKLV-DGICRESLAFETA 671
L + +TH + LP K++ A +LD G T+ V DG +S A
Sbjct: 722 LTLFATHYFELTQLPEKMEGVA-----NVHLDALEHGDTIAFMHSVQDGAASKSYGLAVA 776
Query: 672 KREGVPETIIQRA 684
GVP+ +I+RA
Sbjct: 777 ALAGVPKEVIKRA 789
>pdb|1E3M|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With
A G:t Mismatch
pdb|1E3M|B Chain B, The Crystal Structure Of E. Coli Muts Binding To Dna With
A G:t Mismatch
Length = 800
Score = 94.7 bits (234), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 67/193 (34%), Positives = 92/193 (47%), Gaps = 11/193 (5%)
Query: 498 NTVDMQSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYD 557
N + ++TGPN GGKS+ R +L G VPA+ I D I + + D
Sbjct: 602 NLSPQRRXLIITGPNXGGKSTYXRQTALIALXAYIGSYVPAQKVEIGPIDRIFTRVGAAD 661
Query: 558 SPADGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIETLDN-IGC 616
A G+S+F VE +E +I+ T SLVL DEI RGT T G +A + E L N I
Sbjct: 662 DLASGRSTFXVEXTETANILHNATEYSLVLXDEIGRGTSTYDGLSLAWACAENLANKIKA 721
Query: 617 LGIVSTHLHGIFSLPLKIKNAAYKAMGTEYLD----GQTVPTWKLV-DGICRESLAFETA 671
L + +TH + LP K + A +LD G T+ V DG +S A
Sbjct: 722 LTLFATHYFELTQLPEKXEGVA-----NVHLDALEHGDTIAFXHSVQDGAASKSYGLAVA 776
Query: 672 KREGVPETIIQRA 684
GVP+ +I+RA
Sbjct: 777 ALAGVPKEVIKRA 789
>pdb|3THW|B Chain B, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|B Chain B, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|B Chain B, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|B Chain B, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 918
Score = 89.7 bits (221), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 62/203 (30%), Positives = 102/203 (50%), Gaps = 22/203 (10%)
Query: 501 DMQSLFLLTGPNGGGKSSLLRSICAASLLGICGLMVPAESASIPYFDAIMLHMKSYDSPA 560
D + + ++TGPN GGKSS ++ + +++ G VPAE A+I D I M + D+
Sbjct: 671 DSERVMIITGPNMGGKSSYIKQVALITIMAQIGSYVPAEEATIGIVDGIFTRMGAADNIY 730
Query: 561 DGKSSFQVEMSEIRSIVTATTSRSLVLIDEICRGTETAKGTCIAGSIIET-LDNIGCLGI 619
G+S+F E+++ I+ TS+SLV++DE+ RGT T G IA + +E + ++ L +
Sbjct: 731 KGRSTFMEELTDTAEIIRKATSQSLVILDELGRGTSTHDGIAIAYATLEYFIRDVKSLTL 790
Query: 620 VSTHLHGIFSLPLKIKNAAYKA----MG------TEYLD---GQTVPT-----WKLVDGI 661
TH + L KN +++ MG LD + VP +++ GI
Sbjct: 791 FVTHYPPVCELE---KNYSHQVGNYHMGFLVSEDESKLDPGAAEQVPDFVTFLYQITRGI 847
Query: 662 CRESLAFETAKREGVPETIIQRA 684
S AK VP I+++A
Sbjct: 848 AARSYGLNVAKLADVPGEILKKA 870
>pdb|4AQ4|A Chain A, Substrate Bound Sn-Glycerol-3-Phosphate Binding
Periplasmic Protein Ugpb From Escherichia Coli
Length = 419
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 700 AREQPPPSIIGASCVYVMLRPDKKLYIGQTDDLDGRIRAHRGKEGMQSASFL 751
A++ P +IIG + ++VM DK+ Y G LD + E Q +L
Sbjct: 277 AKDAPQNAIIGGASLWVMQGKDKETYTGVAKFLDFLAKPENAAEWHQKTGYL 328
>pdb|3TR0|A Chain A, Structure Of Guanylate Kinase (Gmk) From Coxiella Burnetii
Length = 205
Score = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 11/29 (37%), Positives = 21/29 (72%)
Query: 498 NTVDMQSLFLLTGPNGGGKSSLLRSICAA 526
N + +LF+++ P+G GK+SL+R++ A
Sbjct: 2 NAXNKANLFIISAPSGAGKTSLVRALVKA 30
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.136 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,806,391
Number of Sequences: 62578
Number of extensions: 908733
Number of successful extensions: 2394
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2366
Number of HSP's gapped (non-prelim): 19
length of query: 803
length of database: 14,973,337
effective HSP length: 107
effective length of query: 696
effective length of database: 8,277,491
effective search space: 5761133736
effective search space used: 5761133736
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)