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= 006859
(628 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 196 bits (498), Expect = 4e-50, Method: Compositional matrix adjust.
Identities = 99/225 (44%), Positives = 143/225 (63%), Gaps = 3/225 (1%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHND-FIPNNIFISEAANMVIVTGPNMSGKSTYLQQ 401
YT P F + + I GRHP++E + N+ FI N + +S M+I+TGPNM GKSTY++Q
Sbjct: 567 YTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQ 626
Query: 402 VCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSE 461
LI ++A IG YVPA I +DRIFTR+G D+L S STFM EM ETA ++ N +E
Sbjct: 627 TALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE 686
Query: 462 RSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFASHMENLSELATIYPNVKILH 520
SL++MDE+GR TS+ DG ++AW+C E+L + +KA T+FA+H L++L V +H
Sbjct: 687 YSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVH 746
Query: 521 FYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETAR 565
+ + + F ++DG YGL +A +AG+P VI+ AR
Sbjct: 747 LDALEHGDTIAFMHSVQDGAAS-KSYGLAVAALAGVPKEVIKRAR 790
>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 = 196 bits (497), Expect = 4e-50, Method: Compositional matrix adjust.
Identities = 99/225 (44%), Positives = 143/225 (63%), Gaps = 3/225 (1%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHND-FIPNNIFISEAANMVIVTGPNMSGKSTYLQQ 401
YT P F + + I GRHP++E + N+ FI N + +S M+I+TGPNM GKSTY++Q
Sbjct: 567 YTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQ 626
Query: 402 VCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSE 461
LI ++A IG YVPA I +DRIFTR+G D+L S STFM EM ETA ++ N +E
Sbjct: 627 TALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE 686
Query: 462 RSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFASHMENLSELATIYPNVKILH 520
SL++MDE+GR TS+ DG ++AW+C E+L + +KA T+FA+H L++L V +H
Sbjct: 687 YSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVH 746
Query: 521 FYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETAR 565
+ + + F ++DG YGL +A +AG+P VI+ AR
Sbjct: 747 LDALEHGDTIAFMHSVQDGAAS-KSYGLAVAALAGVPKEVIKRAR 790
>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 = 196 bits (497), Expect = 4e-50, Method: Compositional matrix adjust.
Identities = 99/225 (44%), Positives = 143/225 (63%), Gaps = 3/225 (1%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHND-FIPNNIFISEAANMVIVTGPNMSGKSTYLQQ 401
YT P F + + I GRHP++E + N+ FI N + +S M+I+TGPNM GKSTY++Q
Sbjct: 567 YTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQ 626
Query: 402 VCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSE 461
LI ++A IG YVPA I +DRIFTR+G D+L S STFM EM ETA ++ N +E
Sbjct: 627 TALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE 686
Query: 462 RSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFASHMENLSELATIYPNVKILH 520
SL++MDE+GR TS+ DG ++AW+C E+L + +KA T+FA+H L++L V +H
Sbjct: 687 YSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVH 746
Query: 521 FYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETAR 565
+ + + F ++DG YGL +A +AG+P VI+ AR
Sbjct: 747 LDALEHGDTIAFMHSVQDGAAS-KSYGLAVAALAGVPKEVIKRAR 790
>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 = 196 bits (497), Expect = 4e-50, Method: Compositional matrix adjust.
Identities = 99/225 (44%), Positives = 143/225 (63%), Gaps = 3/225 (1%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHND-FIPNNIFISEAANMVIVTGPNMSGKSTYLQQ 401
YT P F + + I GRHP++E + N+ FI N + +S M+I+TGPNM GKSTY++Q
Sbjct: 567 YTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQ 626
Query: 402 VCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSE 461
LI ++A IG YVPA I +DRIFTR+G D+L S STFM EM ETA ++ N +E
Sbjct: 627 TALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE 686
Query: 462 RSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFASHMENLSELATIYPNVKILH 520
SL++MDE+GR TS+ DG ++AW+C E+L + +KA T+FA+H L++L V +H
Sbjct: 687 YSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVH 746
Query: 521 FYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETAR 565
+ + + F ++DG YGL +A +AG+P VI+ AR
Sbjct: 747 LDALEHGDTIAFMHSVQDGAAS-KSYGLAVAALAGVPKEVIKRAR 790
>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 = 194 bits (492), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 98/225 (43%), Positives = 143/225 (63%), Gaps = 3/225 (1%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHND-FIPNNIFISEAANMVIVTGPNMSGKSTYLQQ 401
YT P F + + I GRHP++E + N+ FI N + +S M+I+TGPNM GKSTY++Q
Sbjct: 566 YTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQ 625
Query: 402 VCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSE 461
LI ++A IG YVPA I +DRIFTR+G D+L S STFM EM ETA ++ N +E
Sbjct: 626 TALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE 685
Query: 462 RSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFASHMENLSELATIYPNVKILH 520
SL++M+E+GR TS+ DG ++AW+C E+L + +KA T+FA+H L++L V +H
Sbjct: 686 YSLVLMNEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVH 745
Query: 521 FYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETAR 565
+ + + F ++DG YGL +A +AG+P VI+ AR
Sbjct: 746 LDALEHGDTIAFMHSVQDGAAS-KSYGLAVAALAGVPKEVIKRAR 789
>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 = 193 bits (490), Expect = 3e-49, Method: Compositional matrix adjust.
Identities = 98/225 (43%), Positives = 142/225 (63%), Gaps = 3/225 (1%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHND-FIPNNIFISEAANMVIVTGPNMSGKSTYLQQ 401
YT P F + + I GRHP++E + N+ FI N + +S M+I+TGPNM GKSTY++Q
Sbjct: 567 YTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQ 626
Query: 402 VCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSE 461
LI ++A IG YVPA I +DRIFTR+G D+L S STFM EM ETA ++ N +E
Sbjct: 627 TALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE 686
Query: 462 RSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFASHMENLSELATIYPNVKILH 520
SL++MDE+G TS+ DG ++AW+C E+L + +KA T+FA+H L++L V +H
Sbjct: 687 YSLVLMDEIGAGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVH 746
Query: 521 FYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETAR 565
+ + + F ++DG YGL +A +AG+P VI+ AR
Sbjct: 747 LDALEHGDTIAFMHSVQDGAAS-KSYGLAVAALAGVPKEVIKRAR 790
>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 = 182 bits (462), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 95/232 (40%), Positives = 142/232 (61%), Gaps = 8/232 (3%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHNDFIPNNIFISEAANMVIVTGPNMSGKSTYLQQV 402
Y RP F + L I GRHP++E +F+PN++ + A +V++TGPNM+GKST+L+Q
Sbjct: 542 YVRPRFGDR--LQIRAGRHPVVER-RTEFVPNDLEM--AHELVLITGPNMAGKSTFLRQT 596
Query: 403 CLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSER 462
LI +LAQ+G +VPA + + + D I+TR+G D+L STFM EM+E A +++ +E
Sbjct: 597 ALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATEN 656
Query: 463 SLIVMDELGRATSSSDGFAIAWSCCEHLLSLKAYTIFASHMENLSELATIYPNVKILHFY 522
SL+++DE+GR TSS DG AIA + E L +AYT+FA+H L+ L P +K LH
Sbjct: 657 SLVLLDEVGRGTSSLDGVAIATAVAEALHERRAYTLFATHYFELTALGL--PRLKNLHVA 714
Query: 523 VVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETARSITSRITKK 574
L F Q+ GP YG+ +A +AGLP V+ AR++ + +
Sbjct: 715 AREEAGGLVFYHQVLPGPASK-SYGVEVAAMAGLPKEVVARARALLQAMAAR 765
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 8/88 (9%)
Query: 1 MNIDATSVRNLEIIEPLHSALWGTSNKKRSLFHMLKTTKTIGGTRLLRANLLQPLKDIET 60
M + ++R LE+ EPL + +LF +L T+T G RLL++ L PL D
Sbjct: 250 MRLPEATLRALEVFEPLRG--------QDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGP 301
Query: 61 INTRLDCLDELMSNEQLFFGLSQFLRKF 88
+ RLD ++ + L G+ + L +
Sbjct: 302 LEARLDRVEGFVREGALREGVRRLLYRL 329
>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 = 181 bits (459), Expect = 1e-45, Method: Compositional matrix adjust.
Identities = 94/225 (41%), Positives = 136/225 (60%), Gaps = 3/225 (1%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHND-FIPNNIFISEAANMVIVTGPNMSGKSTYLQQ 401
YT P F + + I GRHP++E + N+ FI N + +S +I+TGPN GKSTY +Q
Sbjct: 567 YTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRXLIITGPNXGGKSTYXRQ 626
Query: 402 VCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSE 461
LI + A IG YVPA I +DRIFTR+G D+L S STF E ETA ++ N +E
Sbjct: 627 TALIALXAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFXVEXTETANILHNATE 686
Query: 462 RSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFASHMENLSELATIYPNVKILH 520
SL++ DE+GR TS+ DG ++AW+C E+L + +KA T+FA+H L++L V +H
Sbjct: 687 YSLVLXDEIGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKXEGVANVH 746
Query: 521 FYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETAR 565
+ + + F ++DG YGL +A +AG+P VI+ AR
Sbjct: 747 LDALEHGDTIAFXHSVQDGAAS-KSYGLAVAALAGVPKEVIKRAR 790
>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 = 174 bits (441), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 108/304 (35%), Positives = 169/304 (55%), Gaps = 25/304 (8%)
Query: 328 VNSFAHTISTKPVDRYTRPHFTENGP--LAIDGGRHPILESIHND--FIPNNIFISEAAN 383
V SFAH + PV Y RP E G + + RH +E + ++ FIPN+++ +
Sbjct: 605 VVSFAHVSNGAPVP-YVRPAILEKGQGRIILKASRHACVE-VQDEIAFIPNDVYFEKDKQ 662
Query: 384 MV-IVTGPNMSGKSTYLQQVCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNS 442
M I+TGPNM GKSTY++Q +IV++AQIGC+VP + + +VD I R+G D+
Sbjct: 663 MFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLKGV 722
Query: 443 STFMTEMKETAFVMQNVSERSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFAS 501
STFM EM ETA ++++ ++ SLI++DELGR TS+ DGF +AW+ E++ + + A+ +FA+
Sbjct: 723 STFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFAT 782
Query: 502 HMENLSELATIYPNVKILHFYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVI 561
H L+ LA P V LH + L +Q+K G +G+ +AE+A P VI
Sbjct: 783 HFHELTALANQIPTVNNLHVTALTTEETLTMLYQVKKGVCD-QSFGIHVAELANFPKHVI 841
Query: 562 ETARSITSRITKKEVKRMEINCLQY----KQIQMLYHAAQRLICLKYSNQDEESIRHALQ 617
E A+ K +E+ QY + ++ AA++ C Q E+ I+ L
Sbjct: 842 ECAKQ----------KALELEEFQYIGESQGYDIMEPAAKK--CYLEREQGEKIIQEFLS 889
Query: 618 NLKE 621
+K+
Sbjct: 890 KVKQ 893
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 174 bits (441), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 108/304 (35%), Positives = 169/304 (55%), Gaps = 25/304 (8%)
Query: 328 VNSFAHTISTKPVDRYTRPHFTENGP--LAIDGGRHPILESIHND--FIPNNIFISEAAN 383
V SFAH + PV Y RP E G + + RH +E + ++ FIPN+++ +
Sbjct: 605 VVSFAHVSNGAPVP-YVRPAILEKGQGRIILKASRHACVE-VQDEIAFIPNDVYFEKDKQ 662
Query: 384 MV-IVTGPNMSGKSTYLQQVCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNS 442
M I+TGPNM GKSTY++Q +IV++AQIGC+VP + + +VD I R+G D+
Sbjct: 663 MFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDSQLKGV 722
Query: 443 STFMTEMKETAFVMQNVSERSLIVMDELGRATSSSDGFAIAWSCCEHLLS-LKAYTIFAS 501
STFM EM ETA ++++ ++ SLI++DELGR TS+ DGF +AW+ E++ + + A+ +FA+
Sbjct: 723 STFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEYIATKIGAFCMFAT 782
Query: 502 HMENLSELATIYPNVKILHFYVVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVI 561
H L+ LA P V LH + L +Q+K G +G+ +AE+A P VI
Sbjct: 783 HFHELTALANQIPTVNNLHVTALTTEETLTMLYQVKKGVCD-QSFGIHVAELANFPKHVI 841
Query: 562 ETARSITSRITKKEVKRMEINCLQY----KQIQMLYHAAQRLICLKYSNQDEESIRHALQ 617
E A+ K +E+ QY + ++ AA++ C Q E+ I+ L
Sbjct: 842 ECAKQ----------KALELEEFQYIGESQGYDIMEPAAKK--CYLEREQGEKIIQEFLS 889
Query: 618 NLKE 621
+K+
Sbjct: 890 KVKQ 893
>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 = 170 bits (431), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 90/219 (41%), Positives = 131/219 (59%), Gaps = 8/219 (3%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHNDFIPNNIFISEAANMVIVTGPNMSGKSTYLQQV 402
Y RP F + L I GRHP++E +F+PN++ A +V++TGPN +GKST+L+Q
Sbjct: 542 YVRPRFGDR--LQIRAGRHPVVER-RTEFVPNDL--EXAHELVLITGPNXAGKSTFLRQT 596
Query: 403 CLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSER 462
LI +LAQ+G +VPA + + + D I+TR+G D+L STF E +E A +++ +E
Sbjct: 597 ALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFXVEXEEVALILKEATEN 656
Query: 463 SLIVMDELGRATSSSDGFAIAWSCCEHLLSLKAYTIFASHMENLSELATIYPNVKILHFY 522
SL+++DE+GR TSS DG AIA + E L +AYT+FA+H L+ L P +K LH
Sbjct: 657 SLVLLDEVGRGTSSLDGVAIATAVAEALHERRAYTLFATHYFELTALGL--PRLKNLHVA 714
Query: 523 VVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVI 561
L F Q+ GP YG+ +A AGLP V+
Sbjct: 715 AREEAGGLVFYHQVLPGPASK-SYGVEVAAXAGLPKEVV 752
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 2 NIDATSVRNLEIIEPLHSALWGTSNKKRSLFHMLKTTKTIGGTRLLRANLLQPLKDIETI 61
+ ++R LE+ EPL + +LF +L T+T G RLL++ L PL D +
Sbjct: 251 RLPEATLRALEVFEPLRG--------QDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPL 302
Query: 62 NTRLDCLDELMSNEQLFFGLSQFLRKF 88
RLD ++ + L G+ + L +
Sbjct: 303 EARLDRVEGFVREGALREGVRRLLYRL 329
>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 = 170 bits (431), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 90/219 (41%), Positives = 131/219 (59%), Gaps = 8/219 (3%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHNDFIPNNIFISEAANMVIVTGPNMSGKSTYLQQV 402
Y RP F + L I GRHP++E +F+PN++ A +V++TGPN +GKST+L+Q
Sbjct: 542 YVRPRFGDR--LQIRAGRHPVVER-RTEFVPNDL--EXAHELVLITGPNXAGKSTFLRQT 596
Query: 403 CLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSER 462
LI +LAQ+G +VPA + + + D I+TR+G D+L STF E +E A +++ +E
Sbjct: 597 ALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFXVEXEEVALILKEATEN 656
Query: 463 SLIVMDELGRATSSSDGFAIAWSCCEHLLSLKAYTIFASHMENLSELATIYPNVKILHFY 522
SL+++DE+GR TSS DG AIA + E L +AYT+FA+H L+ L P +K LH
Sbjct: 657 SLVLLDEVGRGTSSLDGVAIATAVAEALHERRAYTLFATHYFELTALGL--PRLKNLHVA 714
Query: 523 VVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVI 561
L F Q+ GP YG+ +A AGLP V+
Sbjct: 715 AREEAGGLVFYHQVLPGPASK-SYGVEVAAXAGLPKEVV 752
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 2 NIDATSVRNLEIIEPLHSALWGTSNKKRSLFHMLKTTKTIGGTRLLRANLLQPLKDIETI 61
+ ++R LE+ EPL + +LF +L T+T G RLL++ L PL D +
Sbjct: 251 RLPEATLRALEVFEPLRG--------QDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPL 302
Query: 62 NTRLDCLDELMSNEQLFFGLSQFLRKF 88
RLD ++ + L G+ + L +
Sbjct: 303 EARLDRVEGFVREGALREGVRRLLYRL 329
>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts
pdb|1EWR|B Chain B, Crystal Structure Of Taq Muts
Length = 649
Score = 170 bits (430), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 90/219 (41%), Positives = 131/219 (59%), Gaps = 8/219 (3%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESIHNDFIPNNIFISEAANMVIVTGPNMSGKSTYLQQV 402
Y RP F + L I GRHP++E +F+PN++ A +V++TGPN +GKST+L+Q
Sbjct: 426 YVRPRFGDR--LQIRAGRHPVVER-RTEFVPNDL--EXAHELVLITGPNXAGKSTFLRQT 480
Query: 403 CLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSER 462
LI +LAQ+G +VPA + + + D I+TR+G D+L STF E +E A +++ +E
Sbjct: 481 ALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFXVEXEEVALILKEATEN 540
Query: 463 SLIVMDELGRATSSSDGFAIAWSCCEHLLSLKAYTIFASHMENLSELATIYPNVKILHFY 522
SL+++DE+GR TSS DG AIA + E L +AYT+FA+H L+ L P +K LH
Sbjct: 541 SLVLLDEVGRGTSSLDGVAIATAVAEALHERRAYTLFATHYFELTALGL--PRLKNLHVA 598
Query: 523 VVIRNNRLDFKFQLKDGPRHVPHYGLLLAEVAGLPSTVI 561
L F Q+ GP YG+ +A AGLP V+
Sbjct: 599 AREEAGGLVFYHQVLPGPASK-SYGVEVAAXAGLPKEVV 636
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 2 NIDATSVRNLEIIEPLHSALWGTSNKKRSLFHMLKTTKTIGGTRLLRANLLQPLKDIETI 61
+ ++R LE+ EPL + +LF +L T+T G RLL++ L PL D +
Sbjct: 135 RLPEATLRALEVFEPLRG--------QDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPL 186
Query: 62 NTRLDCLDELMSNEQLFFGLSQFLRKF 88
RLD ++ + L G+ + L +
Sbjct: 187 EARLDRVEGFVREGALREGVRRLLYRL 213
>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 = 169 bits (428), Expect = 4e-42, Method: Compositional matrix adjust.
Identities = 95/242 (39%), Positives = 145/242 (59%), Gaps = 21/242 (8%)
Query: 343 YTRPHFTENGPLAIDGGRHPILESI---HNDFIPNNIFISEAANMV-IVTGPNMSGKSTY 398
Y RP E + I GRHP+++ + + ++PNN +SE + V I+TGPNM GKS+Y
Sbjct: 630 YCRPTVQEERKIVIKNGRHPVIDVLLGEQDQYVPNNTDLSEDSERVMIITGPNMGGKSSY 689
Query: 399 LQQVCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQN 458
++QV LI I+AQIG YVPA +TI +VD IFTRMG DN+ STFM E+ +TA +++
Sbjct: 690 IKQVALITIMAQIGSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIRK 749
Query: 459 VSERSLIVMDELGRATSSSDGFAIAWSCCEHLL-SLKAYTIFASHMENLSELATIYPN-V 516
+ +SL+++DELGR TS+ DG AIA++ E+ + +K+ T+F +H + EL Y + V
Sbjct: 750 ATSQSLVILDELGRGTSTHDGIAIAYATLEYFIRDVKSLTLFVTHYPPVCELEKNYSHQV 809
Query: 517 KILH--FYVVIRNNRLD------------FKFQLKDGPRHVPHYGLLLAEVAGLPSTVIE 562
H F V ++LD F +Q+ G YGL +A++A +P +++
Sbjct: 810 GNYHMGFLVSEDESKLDPGAAEQVPDFVTFLYQITRGIA-ARSYGLNVAKLADVPGEILK 868
Query: 563 TA 564
A
Sbjct: 869 KA 870
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 38/103 (36%), Positives = 54/103 (52%), Gaps = 7/103 (6%)
Query: 1 MNIDATSVRNLEIIEPLHSALWGTSNKKRSLFHMLKTTKTIGGTRLLRANLLQPLKDIET 60
M I+ T++RNLEI++ K SL +L TKT G R L+ + QPL +
Sbjct: 319 MTINGTTLRNLEILQNQTDM-----KTKGSLLWVLDHTKTSFGRRKLKKWVTQPLLKLRE 373
Query: 61 INTRLDCLDELMSNEQLFFG-LSQFLRKFPKETDRVLCHFCFK 102
IN RLD + E++ +E FG + LRK P + +R LC K
Sbjct: 374 INARLDAVSEVLHSESSVFGQIENHLRKLP-DIERGLCSIYHK 415
>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 = 145 bits (366), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 84/231 (36%), Positives = 128/231 (55%), Gaps = 23/231 (9%)
Query: 354 LAIDGGRHPILES--IHNDFIPNNIFI--------SEAANMVIVTGPNMSGKSTYLQQVC 403
L + G RHP + +DFIPN+I I + A V+VTGPNM GKST ++Q
Sbjct: 751 LELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAG 810
Query: 404 LIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSSTFMTEMKETAFVMQNVSERS 463
L+ ++AQ+GCYVPA + +DR+FTR+G D + S STF E+ ETA ++ + + S
Sbjct: 811 LLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHS 870
Query: 464 LIVMDELGRATSSSDGFAIAWSCCEHLL-SLKAYTIFASHMENLSELATIYPNVKILHFY 522
L+++DELGR T++ DG AIA + + L ++K T+F++H +L E + V++ H
Sbjct: 871 LVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMA 930
Query: 523 VVIRNNRLD---------FKFQLKDGPRHVPHYGLLLAEVAGLPSTVIETA 564
++ N D +KF P+ YG A +A LP VI+
Sbjct: 931 CMVENECEDPSQETITFLYKFIKGACPK---SYGFNAARLANLPEEVIQKG 978
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 59/121 (48%), Gaps = 19/121 (15%)
Query: 1 MNIDATSVRNLEIIEPLHSALWGTSNK-KRSLFHMLKTTKTIGGTRLLRANLLQPLKDIE 59
M +DA ++ NLEI L GT+ + +L + T T G RLL+ L PL +
Sbjct: 395 MVLDAVTLNNLEIF------LNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHY 448
Query: 60 TINTRLDCLDELMSNEQLFFGLSQFLRKFPKETDRVLCHFCFKPKKVTSKVLDVDNAKKS 119
IN RLD +++LM + + L+K P + +R+L SK+ +V + KS
Sbjct: 449 AINDRLDAIEDLMVVPDKISEVVELLKKLP-DLERLL-----------SKIHNVGSPLKS 496
Query: 120 Q 120
Q
Sbjct: 497 Q 497
>pdb|2GA8|A Chain A, Crystal Structure Of Yfh7 From Saccharomyces Cerevisiae: A
Putative P-Loop Containing Kinase With A Circular
Permutation.
pdb|2GAA|A Chain A, Crystal Structure Of Yfh7 From Saccharomyces Cerevisiae: A
Putative P-Loop Containing Kinase With A Circular
Permutation
Length = 359
Score = 29.3 bits (64), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 385 VIVTGPNMSGKSTYLQQVCLIVILAQIGCYVPAHFSTIRVVDRIFTRMGTVDNLESNSST 444
VI+ G SGKST +++ I I + ++ H + I V DR+ + VD+L++
Sbjct: 27 VILVGSPGSGKSTIAEELXQI-INEKYHTFLSEHPNVIEVNDRLKPMVNLVDSLKTLQPN 85
Query: 445 FMTEMKE 451
+ EM E
Sbjct: 86 KVAEMIE 92
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
0.322 0.136 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,382,910
Number of Sequences: 62578
Number of extensions: 551204
Number of successful extensions: 1355
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1301
Number of HSP's gapped (non-prelim): 23
length of query: 628
length of database: 14,973,337
effective HSP length: 105
effective length of query: 523
effective length of database: 8,402,647
effective search space: 4394584381
effective search space used: 4394584381
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)