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= 003142
(844 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 105 bits (263), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 69/199 (34%), Positives = 106/199 (53%), Gaps = 20/199 (10%)
Query: 456 RVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQS 515
RV++ITGPN GGK+ +K V L +MA+ G ++ + E A + D +F +G ++ +
Sbjct: 674 RVMIITGPNMGGKSSYIKQVALITIMAQIGSYVPAEE-ATIGIVDGIFTRMGAADNIYKG 732
Query: 516 LSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAFAESGSLLTIAT 575
STF L II ++TSQSLV+LDE+G GT+ +G A+ + LE F LT+
Sbjct: 733 RSTFMEELTDTAEIIRKATSQSLVILDELGRGTSTHDGIAIAYATLEYFIRDVKSLTLFV 792
Query: 576 THHGELKTLK--YSNDFFENACMEF----DEVKLKP------------TYKILWGVPGRS 617
TH+ + L+ YS+ N M F DE KL P Y+I G+ RS
Sbjct: 793 THYPPVCELEKNYSHQ-VGNYHMGFLVSEDESKLDPGAAEQVPDFVTFLYQITRGIAARS 851
Query: 618 SAINIAERLGLPGIVVQNA 636
+N+A+ +PG +++ A
Sbjct: 852 YGLNVAKLADVPGEILKKA 870
>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 = 98.6 bits (244), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 65/201 (32%), Positives = 107/201 (53%), Gaps = 4/201 (1%)
Query: 445 VPIDIFIARKTRVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFA 504
VP D+ +A + +++ITGPN GK+ L+ L ++A+ G + +E A +P FD ++
Sbjct: 568 VPNDLEMAHE--LVLITGPNMAGKSTFLRQTALIALLAQVG-SFVPAEEAHLPLFDGIYT 624
Query: 505 DIGDEQSLSQSLSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAF 564
IG L+ STF ++++ I+ ++T SLVLLDE+G GT+ L+G A+ ++ EA
Sbjct: 625 RIGASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEAL 684
Query: 565 AESGSLLTIATTHHGELKTLKYSNDFFENACMEFDEVKLKPTYKILWGVPGRSSAINIAE 624
E + T+ TH+ EL L + + L +++L G +S + +A
Sbjct: 685 HERRA-YTLFATHYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLPGPASKSYGVEVAA 743
Query: 625 RLGLPGIVVQNARQLYGAASA 645
GLP VV AR L A +A
Sbjct: 744 MAGLPKEVVARARALLQAMAA 764
>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 = 93.2 bits (230), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 58/187 (31%), Positives = 95/187 (50%), Gaps = 7/187 (3%)
Query: 456 RVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQS 515
R+L+ITGPN GGK+ ++ L +MA G ++ ++ ++ D +F +G L+
Sbjct: 608 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYV-PAQKVEIGPIDRIFTRVGAADDLASG 666
Query: 516 LSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAFAESGSLLTIAT 575
STF + + NI+ +T SLVL+DEIGAGT+ +G +L + E A LT+
Sbjct: 667 RSTFMVEMTETANILHNATEYSLVLMDEIGAGTSTYDGLSLAWACAENLANKIKALTLFA 726
Query: 576 THHGELKTLKYSNDFFENACMEFDEVKLKPTYKILW----GVPGRSSAINIAERLGLPGI 631
TH+ EL L + N + D ++ T + G +S + +A G+P
Sbjct: 727 THYFELTQLPEKMEGVAN--VHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKE 784
Query: 632 VVQNARQ 638
V++ ARQ
Sbjct: 785 VIKRARQ 791
>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 = 93.2 bits (230), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 61/212 (28%), Positives = 102/212 (48%), Gaps = 20/212 (9%)
Query: 445 VPIDIFIA--------RKTRVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKV 496
+P DI I K +++TGPN GGK+ ++ GL +MA+ G ++ +E ++
Sbjct: 771 IPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYV-PAEVCRL 829
Query: 497 PWFDSVFADIGDEQSLSQSLSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTAL 556
D VF +G + STF L + +I+ +T+ SLVL+DE+G GT +GTA+
Sbjct: 830 TPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAI 889
Query: 557 GMSLLEAFAESGSLLTIATTHHGELKTLKYSND----------FFENACMEFDEVKLKPT 606
++++ AE+ T+ +TH+ L YS + EN C + + +
Sbjct: 890 ANAVVKELAETIKCRTLFSTHYHSL-VEDYSQNVAVRLGHMACMVENECEDPSQETITFL 948
Query: 607 YKILWGVPGRSSAINIAERLGLPGIVVQNARQ 638
YK + G +S N A LP V+Q +
Sbjct: 949 YKFIKGACPKSYGFNAARLANLPEEVIQKGHR 980
>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts
pdb|1EWR|B Chain B, Crystal Structure Of Taq Muts
Length = 649
Score = 91.7 bits (226), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 60/189 (31%), Positives = 99/189 (52%), Gaps = 4/189 (2%)
Query: 445 VPIDIFIARKTRVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFA 504
VP D+ A + +++ITGPN GK+ L+ L ++A+ G + +E A +P FD ++
Sbjct: 452 VPNDLEXAHE--LVLITGPNXAGKSTFLRQTALIALLAQVG-SFVPAEEAHLPLFDGIYT 508
Query: 505 DIGDEQSLSQSLSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAF 564
IG L+ STF +++ I+ ++T SLVLLDE+G GT+ L+G A+ ++ EA
Sbjct: 509 RIGASDDLAGGKSTFXVEXEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEAL 568
Query: 565 AESGSLLTIATTHHGELKTLKYSNDFFENACMEFDEVKLKPTYKILWGVPGRSSAINIAE 624
E + T+ TH+ EL L + + L +++L G +S + +A
Sbjct: 569 HERRA-YTLFATHYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLPGPASKSYGVEVAA 627
Query: 625 RLGLPGIVV 633
GLP VV
Sbjct: 628 XAGLPKEVV 636
>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 = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 60/189 (31%), Positives = 99/189 (52%), Gaps = 4/189 (2%)
Query: 445 VPIDIFIARKTRVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFA 504
VP D+ A + +++ITGPN GK+ L+ L ++A+ G + +E A +P FD ++
Sbjct: 568 VPNDLEXAHE--LVLITGPNXAGKSTFLRQTALIALLAQVG-SFVPAEEAHLPLFDGIYT 624
Query: 505 DIGDEQSLSQSLSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAF 564
IG L+ STF +++ I+ ++T SLVLLDE+G GT+ L+G A+ ++ EA
Sbjct: 625 RIGASDDLAGGKSTFXVEXEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEAL 684
Query: 565 AESGSLLTIATTHHGELKTLKYSNDFFENACMEFDEVKLKPTYKILWGVPGRSSAINIAE 624
E + T+ TH+ EL L + + L +++L G +S + +A
Sbjct: 685 HERRA-YTLFATHYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLPGPASKSYGVEVAA 743
Query: 625 RLGLPGIVV 633
GLP VV
Sbjct: 744 XAGLPKEVV 752
>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 = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 57/187 (30%), Positives = 94/187 (50%), Gaps = 7/187 (3%)
Query: 456 RVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQS 515
R+L+ITGPN GGK+ ++ L +MA G ++ ++ ++ D +F +G L+
Sbjct: 608 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYV-PAQKVEIGPIDRIFTRVGAADDLASG 666
Query: 516 LSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAFAESGSLLTIAT 575
STF + + NI+ +T SLVL+DEIG GT+ +G +L + E A LT+
Sbjct: 667 RSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFA 726
Query: 576 THHGELKTLKYSNDFFENACMEFDEVKLKPTYKILW----GVPGRSSAINIAERLGLPGI 631
TH+ EL L + N + D ++ T + G +S + +A G+P
Sbjct: 727 THYFELTQLPEKMEGVAN--VHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKE 784
Query: 632 VVQNARQ 638
V++ ARQ
Sbjct: 785 VIKRARQ 791
>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 = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 57/187 (30%), Positives = 94/187 (50%), Gaps = 7/187 (3%)
Query: 456 RVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQS 515
R+L+ITGPN GGK+ ++ L +MA G ++ ++ ++ D +F +G L+
Sbjct: 608 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYV-PAQKVEIGPIDRIFTRVGAADDLASG 666
Query: 516 LSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAFAESGSLLTIAT 575
STF + + NI+ +T SLVL+DEIG GT+ +G +L + E A LT+
Sbjct: 667 RSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFA 726
Query: 576 THHGELKTLKYSNDFFENACMEFDEVKLKPTYKILW----GVPGRSSAINIAERLGLPGI 631
TH+ EL L + N + D ++ T + G +S + +A G+P
Sbjct: 727 THYFELTQLPEKMEGVAN--VHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKE 784
Query: 632 VVQNARQ 638
V++ ARQ
Sbjct: 785 VIKRARQ 791
>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 = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 57/187 (30%), Positives = 94/187 (50%), Gaps = 7/187 (3%)
Query: 456 RVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQS 515
R+L+ITGPN GGK+ ++ L +MA G ++ ++ ++ D +F +G L+
Sbjct: 608 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYV-PAQKVEIGPIDRIFTRVGAADDLASG 666
Query: 516 LSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAFAESGSLLTIAT 575
STF + + NI+ +T SLVL+DEIG GT+ +G +L + E A LT+
Sbjct: 667 RSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFA 726
Query: 576 THHGELKTLKYSNDFFENACMEFDEVKLKPTYKILW----GVPGRSSAINIAERLGLPGI 631
TH+ EL L + N + D ++ T + G +S + +A G+P
Sbjct: 727 THYFELTQLPEKMEGVAN--VHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKE 784
Query: 632 VVQNARQ 638
V++ ARQ
Sbjct: 785 VIKRARQ 791
>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 = 91.3 bits (225), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 57/187 (30%), Positives = 94/187 (50%), Gaps = 7/187 (3%)
Query: 456 RVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQS 515
R+L+ITGPN GGK+ ++ L +MA G ++ ++ ++ D +F +G L+
Sbjct: 608 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYV-PAQKVEIGPIDRIFTRVGAADDLASG 666
Query: 516 LSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAFAESGSLLTIAT 575
STF + + NI+ +T SLVL+DEIG GT+ +G +L + E A LT+
Sbjct: 667 RSTFMVEMTETANILHNATEYSLVLMDEIGRGTSTYDGLSLAWACAENLANKIKALTLFA 726
Query: 576 THHGELKTLKYSNDFFENACMEFDEVKLKPTYKILW----GVPGRSSAINIAERLGLPGI 631
TH+ EL L + N + D ++ T + G +S + +A G+P
Sbjct: 727 THYFELTQLPEKMEGVAN--VHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKE 784
Query: 632 VVQNARQ 638
V++ ARQ
Sbjct: 785 VIKRARQ 791
>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 = 90.9 bits (224), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 60/189 (31%), Positives = 99/189 (52%), Gaps = 4/189 (2%)
Query: 445 VPIDIFIARKTRVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFA 504
VP D+ A + +++ITGPN GK+ L+ L ++A+ G + +E A +P FD ++
Sbjct: 568 VPNDLEXAHE--LVLITGPNXAGKSTFLRQTALIALLAQVG-SFVPAEEAHLPLFDGIYT 624
Query: 505 DIGDEQSLSQSLSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAF 564
IG L+ STF +++ I+ ++T SLVLLDE+G GT+ L+G A+ ++ EA
Sbjct: 625 RIGASDDLAGGKSTFXVEXEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATAVAEAL 684
Query: 565 AESGSLLTIATTHHGELKTLKYSNDFFENACMEFDEVKLKPTYKILWGVPGRSSAINIAE 624
E + T+ TH+ EL L + + L +++L G +S + +A
Sbjct: 685 HERRA-YTLFATHYFELTALGLPRLKNLHVAAREEAGGLVFYHQVLPGPASKSYGVEVAA 743
Query: 625 RLGLPGIVV 633
GLP VV
Sbjct: 744 XAGLPKEVV 752
>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 = 89.0 bits (219), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 56/187 (29%), Positives = 94/187 (50%), Gaps = 7/187 (3%)
Query: 456 RVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQS 515
R+L+ITGPN GGK+ ++ L +MA G ++ ++ ++ D +F +G L+
Sbjct: 607 RMLIITGPNMGGKSTYMRQTALIALMAYIGSYV-PAQKVEIGPIDRIFTRVGAADDLASG 665
Query: 516 LSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAFAESGSLLTIAT 575
STF + + NI+ +T SLVL++EIG GT+ +G +L + E A LT+
Sbjct: 666 RSTFMVEMTETANILHNATEYSLVLMNEIGRGTSTYDGLSLAWACAENLANKIKALTLFA 725
Query: 576 THHGELKTLKYSNDFFENACMEFDEVKLKPTYKILW----GVPGRSSAINIAERLGLPGI 631
TH+ EL L + N + D ++ T + G +S + +A G+P
Sbjct: 726 THYFELTQLPEKMEGVAN--VHLDALEHGDTIAFMHSVQDGAASKSYGLAVAALAGVPKE 783
Query: 632 VVQNARQ 638
V++ ARQ
Sbjct: 784 VIKRARQ 790
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 87.4 bits (215), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 56/197 (28%), Positives = 99/197 (50%), Gaps = 4/197 (2%)
Query: 445 VPIDIFIARKTRVL-VITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVF 503
+P D++ + ++ +ITGPN GGK+ ++ G+ V+MA+ G + E A+V D +
Sbjct: 651 IPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFV-PCESAEVSIVDCIL 709
Query: 504 ADIGDEQSLSQSLSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEA 563
A +G S + +STF + + +I+ +T SL+++DE+G GT+ +G L ++ E
Sbjct: 710 ARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEY 769
Query: 564 FAESGSLLTIATTHHGELKTLKYSNDFFENACMEFDEVKLKPT--YKILWGVPGRSSAIN 621
A + TH EL L N + + T Y++ GV +S I+
Sbjct: 770 IATKIGAFCMFATHFHELTALANQIPTVNNLHVTALTTEETLTMLYQVKKGVCDQSFGIH 829
Query: 622 IAERLGLPGIVVQNARQ 638
+AE P V++ A+Q
Sbjct: 830 VAELANFPKHVIECAKQ 846
>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 = 87.0 bits (214), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 56/197 (28%), Positives = 99/197 (50%), Gaps = 4/197 (2%)
Query: 445 VPIDIFIARKTRVL-VITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVF 503
+P D++ + ++ +ITGPN GGK+ ++ G+ V+MA+ G + E A+V D +
Sbjct: 651 IPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIVLMAQIGCFV-PCESAEVSIVDCIL 709
Query: 504 ADIGDEQSLSQSLSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEA 563
A +G S + +STF + + +I+ +T SL+++DE+G GT+ +G L ++ E
Sbjct: 710 ARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDELGRGTSTYDGFGLAWAISEY 769
Query: 564 FAESGSLLTIATTHHGELKTLKYSNDFFENACMEFDEVKLKPT--YKILWGVPGRSSAIN 621
A + TH EL L N + + T Y++ GV +S I+
Sbjct: 770 IATKIGAFCMFATHFHELTALANQIPTVNNLHVTALTTEETLTMLYQVKKGVCDQSFGIH 829
Query: 622 IAERLGLPGIVVQNARQ 638
+AE P V++ A+Q
Sbjct: 830 VAELANFPKHVIECAKQ 846
>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 = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 56/185 (30%), Positives = 88/185 (47%), Gaps = 3/185 (1%)
Query: 456 RVLVITGPNTGGKTICLKTVGLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQS 515
R L+ITGPN GGK+ + L + A G ++ + + P D +F +G L+
Sbjct: 608 RXLIITGPNXGGKSTYXRQTALIALXAYIGSYVPAQKVEIGP-IDRIFTRVGAADDLASG 666
Query: 516 LSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTALGMSLLEAFAESGSLLTIAT 575
STF + NI+ +T SLVL DEIG GT+ +G +L + E A LT+
Sbjct: 667 RSTFXVEXTETANILHNATEYSLVLXDEIGRGTSTYDGLSLAWACAENLANKIKALTLFA 726
Query: 576 THHGELKTLKYSNDFFENACMEFDE--VKLKPTYKILWGVPGRSSAINIAERLGLPGIVV 633
TH+ EL L + N ++ E + + + G +S + +A G+P V+
Sbjct: 727 THYFELTQLPEKXEGVANVHLDALEHGDTIAFXHSVQDGAASKSYGLAVAALAGVPKEVI 786
Query: 634 QNARQ 638
+ ARQ
Sbjct: 787 KRARQ 791
>pdb|2GEJ|A Chain A, Crystal Structure Of Phosphatidylinositol
Mannosyltransferase (Pima) From Mycobacterium Smegmatis
In Complex With Gdp-Man
pdb|2GEK|A Chain A, Crystal Structure Of Phosphatidylinositol
Mannosyltransferase (Pima) From Mycobacterium Smegmatis
In Complex With Gdp
Length = 406
Score = 31.6 bits (70), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 476 GLAVMMAKSGLHILSSEYAKVPWFDSVFADIGDEQSLSQSLSTFSGHLKQIGNIISQSTS 535
G+AV++A L A+ P + + GDE L + +GHL+ +G + + +
Sbjct: 223 GMAVLLAA-----LPKLVARFPDVEILIVGRGDEDELREQAGDLAGHLRFLGQVDDATKA 277
Query: 536 QSLVLLDEIGAGTNPLEGTALGMSLLEAFA 565
++ D A L G + G+ L+EA A
Sbjct: 278 SAMRSADVYCA--PHLGGESFGIVLVEAMA 305
>pdb|3A0G|B Chain B, Crystal Structure Analysis Of Guinea Pig Oxyhemoglobin At
2.5 Angstroms Resolution
Length = 146
Score = 30.8 bits (68), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 39/91 (42%), Gaps = 18/91 (19%)
Query: 497 PWFDSVFADIGDEQSLSQSLSTFSGHLKQIGNIISQSTSQSLVLLDEIGAGTNPLEGTAL 556
PW F GD S S +S + H+K G + S S+ L L + L+GT
Sbjct: 36 PWTQRFFEKFGDLSSASAIMS--NAHVKSHGAKVLASFSEGLKHLQD-------LKGTFA 86
Query: 557 GMSLL---------EAFAESGSLLTIATTHH 578
+S L E F G++LTIA HH
Sbjct: 87 KLSELHCDKLHVDPENFRLLGNMLTIAIAHH 117
>pdb|3QQC|D Chain D, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 163
Score = 29.6 bits (65), Expect = 8.0, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 22/31 (70%), Gaps = 3/31 (9%)
Query: 801 GDLVHVSS---FGKKGTVIKVEPSKEEIVVQ 828
GDLV V + G+K V+K++ SK+E+VVQ
Sbjct: 95 GDLVEVIAGPFKGQKAKVVKIDESKDEVVVQ 125
>pdb|2PK3|A Chain A, Crystal Structure Of A Gdp-4-Keto-6-Deoxy-D-Mannose
Reductase
pdb|2PK3|B Chain B, Crystal Structure Of A Gdp-4-Keto-6-Deoxy-D-Mannose
Reductase
Length = 321
Score = 29.3 bits (64), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 14/54 (25%)
Query: 802 DLVHVSSFGKKGT--------------VIKVEPSKEEIVVQVGNMKWIMKFTDI 841
D++H +F G ++ +E K+E +++VGN++ + FTD+
Sbjct: 173 DIIHTRTFNHIGPGQSLGFVTQDFAKQIVDIEMEKQEPIIKVGNLEAVRDFTDV 226
>pdb|3P8B|B Chain B, X-Ray Crystal Structure Of Pyrococcus Furiosus
Transcription Elongation Factor Spt45
pdb|3P8B|D Chain D, X-Ray Crystal Structure Of Pyrococcus Furiosus
Transcription Elongation Factor Spt45
Length = 152
Score = 29.3 bits (64), Expect = 9.1, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 22/31 (70%), Gaps = 3/31 (9%)
Query: 801 GDLVHVSS---FGKKGTVIKVEPSKEEIVVQ 828
GDLV V + G+K V+K++ SK+E+VVQ
Sbjct: 95 GDLVEVIAGPFKGQKAKVVKIDESKDEVVVQ 125
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.130 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,841,391
Number of Sequences: 62578
Number of extensions: 763091
Number of successful extensions: 2081
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2021
Number of HSP's gapped (non-prelim): 40
length of query: 844
length of database: 14,973,337
effective HSP length: 107
effective length of query: 737
effective length of database: 8,277,491
effective search space: 6100510867
effective search space used: 6100510867
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)