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= 001977
(987 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 400 bits (1029), Expect = e-111, Method: Compositional matrix adjust.
Identities = 249/713 (34%), Positives = 382/713 (53%), Gaps = 44/713 (6%)
Query: 278 GDVSERFSAREADKFHFLGPD-RRDAKRRRPGDVYYDPRTLYLPPDFLRNLSEGQKQWWE 336
GD S R + + +L + RRD RRRP +D TLY+P DFL + + G ++WW+
Sbjct: 18 GDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQ 77
Query: 337 FKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMKGEQPHCGFPERNFSMNVEKLAR 396
KS++ D VI +K+GKFYEL+ MDA +G EL L +MKG H GFPE F + L +
Sbjct: 78 IKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQ 137
Query: 397 KGYRVLVVEQTETPEQLELRRKEKG---SKDKVVKREICAVVTKGTLTEGELLSANPD-- 451
KGY+V VEQTETPE +E R ++ D+VV+REIC ++TKGT T +L +P
Sbjct: 138 KGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYS-VLEGDPSEN 196
Query: 452 -ASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQVMXXXXXXXXXXXXXXXRPV 510
+ YL++L E + + + R +G+C VD + + +GQ PV
Sbjct: 197 YSKYLLSLKEKEEDSSGHT--RAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPV 254
Query: 511 EIIKPANMLSPETERAILRHTRNPLVNDLVPLSEFWDAET---TVLEIKNIYNRITAESL 567
+++ LS ET+ + L L+P S+FWDA T+LE + +++
Sbjct: 255 QVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIG 314
Query: 568 NKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTLFYLKKSFLDETLLRF 627
+ +E D + PG SEL LSALGG +FYLKK +D+ LL
Sbjct: 315 VMLPQVLKGMTSESDSIGLTPGEKSEL---------ALSALGGCVFYLKKCLIDQELLSM 365
Query: 628 AKFE--------LLPCSGFGDMAKKPY--MVLDAPALENLEVFENSRSGDSSGTLYAQLN 677
A FE + + G + K Y MVLDA L NLE+F N +G + GTL +++
Sbjct: 366 ANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVD 425
Query: 678 HCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFALEFRKALSRLPDMERLL 737
C T FGKRLL+ WL PL N I +R DA+ L V + E + L +LPD+ERLL
Sbjct: 426 TCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKIS-EVVELLKKLPDLERLL 484
Query: 738 ARLF---ASSEANGRNSNKVVLYEDA--AKKQLQEFISALHGCELMDQACSSLGAILENT 792
+++ + ++ ++ ++YE+ +KK++ +F+SAL G ++M + + + +
Sbjct: 485 SKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGF 544
Query: 793 ESRQLHHILT-----PGKGLPAIVSILKHFKDAFDWVEANNSGRIIPHGGVDMDYDSACK 847
+S+ L +++ P P + L + AFD +A +G I P G D DYD A
Sbjct: 545 KSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALA 604
Query: 848 KVKEIEASLTKHLKEQRKLLGDTSITYVTIGKDLYLLEVPESLRG-SVPRDYELRSSKKG 906
++E E SL ++L++QR +G +I Y IG++ Y LE+PE+ ++P +YEL+S+KKG
Sbjct: 605 DIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKG 664
Query: 907 FFRYWTPNIKKLLGELSQAESEKESALKSILQRLIGQFCEHHNKWRQMVAATA 959
RYWT I+K L L AE ++ +LK ++RL F +++ W+ V A
Sbjct: 665 CKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIA 717
>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 = 134 bits (337), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 141/636 (22%), Positives = 268/636 (42%), Gaps = 70/636 (11%)
Query: 333 QWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQ-YMKGEQPHCGFPERNFSMNV 391
Q+ E K +H D V+ + G Y F DA + A+EL++ ++ P ++V
Sbjct: 19 QYIEMKQQHKDAVLCVECGYKYRFFGEDAEIAARELNIYCHLDHNFMTASIPTHRLFVHV 78
Query: 392 EKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGEL------ 445
+L KGY+V VV+QTET + ++ + R++ A+ TK TL ++
Sbjct: 79 RRLVAKGYKVGVVKQTETAA----LKAIGDNRSSLFSRKLTALYTKSTLIGEDVNPLIKL 134
Query: 446 --------LSANPDASYLMALTESNQSPASQSTDRCF-GICVVDVATSRIILGQVMXXXX 496
+ + SYL+ ++E+ ++ + F GI V AT ++
Sbjct: 135 DDAVNVDEIMTDTSTSYLLCISENKENVRDKKKGNIFIGIVGVQPATGEVVFDSFQDSAS 194
Query: 497 XXXXXXXXXXXRPVEIIKPANMLSPETERAILRHTRNPLVNDLVPLSEFWDAETTVLEIK 556
+PVE++ P+ LS +TE I R T + +D + V +
Sbjct: 195 RSELETRMSSLQPVELLLPS-ALSEQTEALIHRATSVSVQDDRI----------RVERMD 243
Query: 557 NIYNRITAESLNKADSNVANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTLFYLK 616
NIY + + A + G + GI+ + V+ +L + YLK
Sbjct: 244 NIYFEY-SHAFQAVTEFYAKDTVDIKGSQIISGIV-------NLEKPVICSLAAIIKYLK 295
Query: 617 KSFLDETLLRFAKFELLPCSGFGDMAKKPYMVLDAPALENLEVFENSRSGDSSGTLYAQL 676
+ L++ L + F+ L +K +M ++ L NLE+ +N + G+L L
Sbjct: 296 EFNLEKMLSKPENFKQLS-------SKMEFMTINGTTLRNLEILQNQTDMKTKGSLLWVL 348
Query: 677 NHCVTAFGKRLLRTWLARPLYNSGLIRERQDAVAGLRGVNQPFALEFRKALSRLPDMERL 736
+H T+FG+R L+ W+ +PL I R DAV+ + + L +LPD+ER
Sbjct: 349 DHTKTSFGRRKLKKWVTQPLLKLREINARLDAVSEVLHSESSVFGQIENHLRKLPDIERG 408
Query: 737 LARLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCELMDQACSSLGAILENTESRQ 796
L ++ ++ + ++ + L+ + QA + A+ + +S
Sbjct: 409 LCSIY---------------HKKCSTQEFFLIVKTLYHLKSEFQAI--IPAVNSHIQSDL 451
Query: 797 LHHILTPGKGLPAIVSILKHFKDAFDWVEANNSGRIIPHGGVDMDYDSACKKVKEIEASL 856
L ++ +P ++S ++H+ + A + + D+ K+ EI+ +
Sbjct: 452 LRTVILE---IPELLSPVEHYLKILNEQAAKVGDKTELFKDLS-DFPLIKKRKDEIQGVI 507
Query: 857 TK---HLKEQRKLLGDTSITYVTIGKDLYLLEVPESLRGSVPRDYELRSSKKGFFRYWTP 913
+ HL+E RK+L + S YVT+ +++E+ S +P D+ S K R+ +P
Sbjct: 508 DEIRMHLQEIRKILKNPSAQYVTVSGQEFMIEIKNSAVSCIPTDWVKVGSTKAVSRFHSP 567
Query: 914 NIKKLLGELSQAESEKESALKSILQRLIGQFCEHHN 949
I + L+Q + + + +F EH++
Sbjct: 568 FIVENYRHLNQLREQLVLDCSAEWLDFLEKFSEHYH 603
>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 = 67.8 bits (164), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 46/158 (29%), Positives = 76/158 (48%), Gaps = 27/158 (17%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMKGEQ-----PHCGFPERN 386
+Q+ E + ++ D ++ F++G FYE F DA A+ L L P G P R
Sbjct: 18 QQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARALGLVLTHKTSKDFTTPXAGIPLRA 77
Query: 387 FSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGELL 446
F E+L + G+R+ V +Q E E+ E +V+RE+ ++T GTL + LL
Sbjct: 78 FEAYAERLLKXGFRLAVADQVEPAEEAE----------GLVRREVTQLLTPGTLLQESLL 127
Query: 447 SANPDASYLMALTESNQSPASQSTDRCFGICVVDVATS 484
+A+YL A+ +T +G+ +DV+T
Sbjct: 128 PR--EANYLAAI----------ATGDGWGLAFLDVSTG 153
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 57/111 (51%), Gaps = 14/111 (12%)
Query: 639 GDMAKKPYMVLDAPA--------LENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRT 690
G ++ +P+ D A L LEVFE R D TL++ L+ TA G+RLL++
Sbjct: 234 GALSLQPFRFYDPGAFXRLPEATLRALEVFEPLRGQD---TLFSVLDETRTAPGRRLLQS 290
Query: 691 WLARPLYNSGLIRERQDAVAGLRGVNQPFALE-FRKALSRLPDMERLLARL 740
WL PL + G + R D V G V + E R+ L RL D+ERL RL
Sbjct: 291 WLRHPLLDRGPLEARLDRVEGF--VREGALREGVRRLLYRLADLERLATRL 339
>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 = 67.8 bits (164), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 46/158 (29%), Positives = 76/158 (48%), Gaps = 27/158 (17%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMKGEQ-----PHCGFPERN 386
+Q+ E + ++ D ++ F++G FYE F DA A+ L L P G P R
Sbjct: 18 QQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARALGLVLTHKTSKDFTTPXAGIPLRA 77
Query: 387 FSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGELL 446
F E+L + G+R+ V +Q E E+ E +V+RE+ ++T GTL + LL
Sbjct: 78 FEAYAERLLKXGFRLAVADQVEPAEEAE----------GLVRREVTQLLTPGTLLQESLL 127
Query: 447 SANPDASYLMALTESNQSPASQSTDRCFGICVVDVATS 484
+A+YL A+ +T +G+ +DV+T
Sbjct: 128 PR--EANYLAAI----------ATGDGWGLAFLDVSTG 153
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 57/111 (51%), Gaps = 14/111 (12%)
Query: 639 GDMAKKPYMVLDAPA--------LENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRT 690
G ++ +P+ D A L LEVFE R D TL++ L+ TA G+RLL++
Sbjct: 234 GALSLQPFRFYDPGAFXRLPEATLRALEVFEPLRGQD---TLFSVLDETRTAPGRRLLQS 290
Query: 691 WLARPLYNSGLIRERQDAVAGLRGVNQPFALE-FRKALSRLPDMERLLARL 740
WL PL + G + R D V G V + E R+ L RL D+ERL RL
Sbjct: 291 WLRHPLLDRGPLEARLDRVEGF--VREGALREGVRRLLYRLADLERLATRL 339
>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 = 67.0 bits (162), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 46/158 (29%), Positives = 76/158 (48%), Gaps = 27/158 (17%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMKGEQ-----PHCGFPERN 386
+Q+ E + ++ D ++ F++G FYE F DA A+ L L P G P R
Sbjct: 18 QQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARALGLVLTHKTSKDFTTPMAGIPLRA 77
Query: 387 FSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGELL 446
F E+L + G+R+ V +Q E E+ E +V+RE+ ++T GTL + LL
Sbjct: 78 FEAYAERLLKMGFRLAVADQVEPAEEAE----------GLVRREVTQLLTPGTLLQESLL 127
Query: 447 SANPDASYLMALTESNQSPASQSTDRCFGICVVDVATS 484
+A+YL A+ +T +G+ +DV+T
Sbjct: 128 PR--EANYLAAI----------ATGDGWGLAFLDVSTG 153
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/96 (41%), Positives = 52/96 (54%), Gaps = 6/96 (6%)
Query: 646 YMVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRER 705
+M L L LEVFE R D TL++ L+ TA G+RLL++WL PL + G + R
Sbjct: 249 FMRLPEATLRALEVFEPLRGQD---TLFSVLDETRTAPGRRLLQSWLRHPLLDRGPLEAR 305
Query: 706 QDAVAGLRGVNQPFALE-FRKALSRLPDMERLLARL 740
D V G V + E R+ L RL D+ERL RL
Sbjct: 306 LDRVEGF--VREGALREGVRRLLYRLADLERLATRL 339
>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 = 62.0 bits (149), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/165 (27%), Positives = 74/165 (44%), Gaps = 26/165 (15%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMK-----GEQ-PHCGFPER 385
+Q+ K++H + ++F++MG FYELF DA ++ LD+ K GE P G P
Sbjct: 15 QQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYH 74
Query: 386 NFSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGEL 445
+ KL +G V + EQ P KG V+R++ +VT GT+++ L
Sbjct: 75 AVENYLAKLVNQGESVAICEQIGDPA------TSKGP----VERKVVRIVTPGTISDEAL 124
Query: 446 LSANPDASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQ 490
L D N A + FG +D+++ R L +
Sbjct: 125 LQERQD----------NLLAAIWQDSKGFGYATLDISSGRFRLSE 159
Score = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 5/94 (5%)
Query: 647 MVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQ 706
+++DA NLE+ +N +G + TL + L+ VT G R+L+ WL P+ ++ ++ ERQ
Sbjct: 267 IIMDAATRRNLEITQN-LAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQ 325
Query: 707 DAVAGLRGVNQPFALEFRKALSRLPDMERLLARL 740
+ L Q F + L ++ D+ER+LARL
Sbjct: 326 QTIGAL----QDFTAGLQPVLRQVGDLERILARL 355
>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 = 62.0 bits (149), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/165 (27%), Positives = 74/165 (44%), Gaps = 26/165 (15%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMK-----GEQ-PHCGFPER 385
+Q+ K++H + ++F++MG FYELF DA ++ LD+ K GE P G P
Sbjct: 15 QQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYH 74
Query: 386 NFSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGEL 445
+ KL +G V + EQ P KG V+R++ +VT GT+++ L
Sbjct: 75 AVENYLAKLVNQGESVAICEQIGDPA------TSKGP----VERKVVRIVTPGTISDEAL 124
Query: 446 LSANPDASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQ 490
L D N A + FG +D+++ R L +
Sbjct: 125 LQERQD----------NLLAAIWQDSKGFGYATLDISSGRFRLSE 159
Score = 58.2 bits (139), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 5/94 (5%)
Query: 647 MVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQ 706
+++DA NLE+ +N +G + TL + L+ VT G R+L+ WL P+ ++ ++ ERQ
Sbjct: 267 IIMDAATRRNLEITQN-LAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQ 325
Query: 707 DAVAGLRGVNQPFALEFRKALSRLPDMERLLARL 740
+ L Q F + L ++ D+ER+LARL
Sbjct: 326 QTIGAL----QDFTAGLQPVLRQVGDLERILARL 355
>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 = 62.0 bits (149), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/165 (27%), Positives = 74/165 (44%), Gaps = 26/165 (15%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMK-----GEQ-PHCGFPER 385
+Q+ K++H + ++F++MG FYELF DA ++ LD+ K GE P G P
Sbjct: 14 QQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYH 73
Query: 386 NFSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGEL 445
+ KL +G V + EQ P KG V+R++ +VT GT+++ L
Sbjct: 74 AVENYLAKLVNQGESVAICEQIGDPA------TSKGP----VERKVVRIVTPGTISDEAL 123
Query: 446 LSANPDASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQ 490
L D N A + FG +D+++ R L +
Sbjct: 124 LQERQD----------NLLAAIWQDSKGFGYATLDISSGRFRLSE 158
Score = 58.2 bits (139), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 5/94 (5%)
Query: 647 MVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQ 706
+++DA NLE+ +N +G + TL + L+ VT G R+L+ WL P+ ++ ++ ERQ
Sbjct: 266 IIMDAATRRNLEITQN-LAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQ 324
Query: 707 DAVAGLRGVNQPFALEFRKALSRLPDMERLLARL 740
+ L Q F + L ++ D+ER+LARL
Sbjct: 325 QTIGAL----QDFTAGLQPVLRQVGDLERILARL 354
>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 = 60.8 bits (146), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 74/165 (44%), Gaps = 26/165 (15%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMK-----GEQ-PHCGFPER 385
+Q+ K++H + ++F++MG FY+LF DA ++ LD+ K GE P G P
Sbjct: 15 QQYLRLKAQHPEILLFYRMGDFYQLFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYH 74
Query: 386 NFSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGEL 445
+ KL +G V + EQ P KG V+R++ +VT GT+++ L
Sbjct: 75 AVENYLAKLVNQGESVAICEQIGDPA------TSKGP----VERKVVRIVTPGTISDEAL 124
Query: 446 LSANPDASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQ 490
L D N A + FG +D+++ R L +
Sbjct: 125 LQERQD----------NLLAAIWQDSKGFGYATLDISSGRFRLSE 159
Score = 58.2 bits (139), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 5/94 (5%)
Query: 647 MVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQ 706
+++DA NLE+ +N +G + TL + L+ VT G R+L+ WL P+ ++ ++ ERQ
Sbjct: 267 IIMDAATRRNLEITQN-LAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQ 325
Query: 707 DAVAGLRGVNQPFALEFRKALSRLPDMERLLARL 740
+ L Q F + L ++ D+ER+LARL
Sbjct: 326 QTIGAL----QDFTAGLQPVLRQVGDLERILARL 355
>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 = 59.7 bits (143), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 73/165 (44%), Gaps = 26/165 (15%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMK-----GEQ-PHCGFPER 385
+Q+ K++H + ++F++MG FY LF DA ++ LD+ K GE P G P
Sbjct: 15 QQYLRLKAQHPEILLFYRMGDFYTLFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYH 74
Query: 386 NFSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGEL 445
+ KL +G V + EQ P KG V+R++ +VT GT+++ L
Sbjct: 75 AVENYLAKLVNQGESVAICEQIGDPA------TSKGP----VERKVVRIVTPGTISDEAL 124
Query: 446 LSANPDASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQ 490
L D N A + FG +D+++ R L +
Sbjct: 125 LQERQD----------NLLAAIWQDSKGFGYATLDISSGRFRLSE 159
Score = 58.2 bits (139), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 5/94 (5%)
Query: 647 MVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQ 706
+++DA NLE+ +N +G + TL + L+ VT G R+L+ WL P+ ++ ++ ERQ
Sbjct: 267 IIMDAATRRNLEITQN-LAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQ 325
Query: 707 DAVAGLRGVNQPFALEFRKALSRLPDMERLLARL 740
+ L Q F + L ++ D+ER+LARL
Sbjct: 326 QTIGAL----QDFTAGLQPVLRQVGDLERILARL 355
>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 = 59.7 bits (143), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 73/165 (44%), Gaps = 26/165 (15%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMK-----GEQ-PHCGFPER 385
+Q+ K++H + ++F++ G FYELF DA ++ LD+ K GE P G P
Sbjct: 15 QQYLRLKAQHPEILLFYRXGDFYELFYDDAKRASQLLDISLTKRGASAGEPIPXAGIPYH 74
Query: 386 NFSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGEL 445
+ KL +G V + EQ P KG V+R++ +VT GT+++ L
Sbjct: 75 AVENYLAKLVNQGESVAICEQIGDPA------TSKGP----VERKVVRIVTPGTISDEAL 124
Query: 446 LSANPDASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQ 490
L D N A + FG +D+++ R L +
Sbjct: 125 LQERQD----------NLLAAIWQDSKGFGYATLDISSGRFRLSE 159
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 52/94 (55%), Gaps = 5/94 (5%)
Query: 647 MVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQ 706
++ DA NLE+ +N +G + TL + L+ VT G R L+ WL P+ ++ ++ ERQ
Sbjct: 267 IIXDAATRRNLEITQN-LAGGAENTLASVLDCTVTPXGSRXLKRWLHXPVRDTRVLLERQ 325
Query: 707 DAVAGLRGVNQPFALEFRKALSRLPDMERLLARL 740
+ L Q F + L ++ D+ER+LARL
Sbjct: 326 QTIGAL----QDFTAGLQPVLRQVGDLERILARL 355
>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 = 59.7 bits (143), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 73/165 (44%), Gaps = 26/165 (15%)
Query: 332 KQWWEFKSKHMDKVIFFKMGKFYELFEMDAHVGAKELDLQYMK-----GEQ-PHCGFPER 385
+Q+ K++H + ++F++MG FY LF DA ++ LD+ K GE P G P
Sbjct: 15 QQYLRLKAQHPEILLFYRMGDFYALFYDDAKRASQLLDISLTKRGASAGEPIPMAGIPYH 74
Query: 386 NFSMNVEKLARKGYRVLVVEQTETPEQLELRRKEKGSKDKVVKREICAVVTKGTLTEGEL 445
+ KL +G V + EQ P KG V+R++ +VT GT+++ L
Sbjct: 75 AVENYLAKLVNQGESVAICEQIGDPA------TSKGP----VERKVVRIVTPGTISDEAL 124
Query: 446 LSANPDASYLMALTESNQSPASQSTDRCFGICVVDVATSRIILGQ 490
L D N A + FG +D+++ R L +
Sbjct: 125 LQERQD----------NLLAAIWQDSKGFGYATLDISSGRFRLSE 159
Score = 58.2 bits (139), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 5/94 (5%)
Query: 647 MVLDAPALENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRTWLARPLYNSGLIRERQ 706
+++DA NLE+ +N +G + TL + L+ VT G R+L+ WL P+ ++ ++ ERQ
Sbjct: 267 IIMDAATRRNLEITQN-LAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQ 325
Query: 707 DAVAGLRGVNQPFALEFRKALSRLPDMERLLARL 740
+ L Q F + L ++ D+ER+LARL
Sbjct: 326 QTIGAL----QDFTAGLQPVLRQVGDLERILARL 355
>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts
pdb|1EWR|B Chain B, Crystal Structure Of Taq Muts
Length = 649
Score = 53.5 bits (127), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 42/111 (37%), Positives = 57/111 (51%), Gaps = 14/111 (12%)
Query: 639 GDMAKKPYMVLDAPA--------LENLEVFENSRSGDSSGTLYAQLNHCVTAFGKRLLRT 690
G ++ +P+ D A L LEVFE R D TL++ L+ TA G+RLL++
Sbjct: 118 GALSLQPFRFYDPGAFXRLPEATLRALEVFEPLRGQD---TLFSVLDETRTAPGRRLLQS 174
Query: 691 WLARPLYNSGLIRERQDAVAGLRGVNQPFALE-FRKALSRLPDMERLLARL 740
WL PL + G + R D V G V + E R+ L RL D+ERL RL
Sbjct: 175 WLRHPLLDRGPLEARLDRVEGF--VREGALREGVRRLLYRLADLERLATRL 223
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 51.2 bits (121), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 53/158 (33%), Positives = 74/158 (46%), Gaps = 26/158 (16%)
Query: 627 FAKFELLPCSGFGDMAKKPYMVLDAPALENLEVFENSRSGDSSGT--LYAQLNHCVTAFG 684
F +FEL D ++ YM LD A+ L +F+ S D++G+ L A LN C T G
Sbjct: 286 FGQFELTTF----DFSQ--YMKLDIAAVRALNLFQGSVE-DTTGSQSLAALLNKCKTPQG 338
Query: 685 KRLLRTWLARPLYNSGLIRERQDAV------AGLRGVNQPFALEFRKALSRLPDMERLLA 738
+RL+ W+ +PL + I ER + V A LR Q L R PD+ R LA
Sbjct: 339 QRLVNQWIKQPLMDKNRIEERLNLVEAFVEDAELRQTLQ------EDLLRRFPDLNR-LA 391
Query: 739 RLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCE 776
+ F AN ++ + LY+ QL I AL E
Sbjct: 392 KKFQRQAANLQDCYR--LYQ--GINQLPNVIQALEKHE 425
>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 = 51.2 bits (121), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 53/158 (33%), Positives = 74/158 (46%), Gaps = 26/158 (16%)
Query: 627 FAKFELLPCSGFGDMAKKPYMVLDAPALENLEVFENSRSGDSSGT--LYAQLNHCVTAFG 684
F +FEL D ++ YM LD A+ L +F+ S D++G+ L A LN C T G
Sbjct: 286 FGQFELTTF----DFSQ--YMKLDIAAVRALNLFQGSVE-DTTGSQSLAALLNKCKTPQG 338
Query: 685 KRLLRTWLARPLYNSGLIRERQDAV------AGLRGVNQPFALEFRKALSRLPDMERLLA 738
+RL+ W+ +PL + I ER + V A LR Q L R PD+ R LA
Sbjct: 339 QRLVNQWIKQPLMDKNRIEERLNLVEAFVEDAELRQTLQ------EDLLRRFPDLNR-LA 391
Query: 739 RLFASSEANGRNSNKVVLYEDAAKKQLQEFISALHGCE 776
+ F AN ++ + LY+ QL I AL E
Sbjct: 392 KKFQRQAANLQDCYR--LYQ--GINQLPNVIQALEKHE 425
>pdb|1LLW|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Complex With
2-Oxoglutarate
pdb|1LLZ|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Reduced Enzyme
pdb|1LM1|A Chain A, Structural Studies On The Synchronization Of Catalytic
Centers In Glutamate Synthase: Native Enzyme
pdb|1OFD|A Chain A, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate At 2.0 Angstrom Resolution
pdb|1OFD|B Chain B, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate At 2.0 Angstrom Resolution
pdb|1OFE|A Chain A, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate And L-Don At 2.45 Angstrom Resolution
pdb|1OFE|B Chain B, Glutamate Synthase From Synechocystis Sp In Complex With
2-Oxoglutarate And L-Don At 2.45 Angstrom Resolution
Length = 1520
Score = 36.2 bits (82), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 38/150 (25%), Positives = 62/150 (41%), Gaps = 13/150 (8%)
Query: 514 KPANMLSPETERAILRHTRNPLVNDLVPLSEFWDAETTVLEIKNIYNRITAESLNKADSN 573
K N+L P+ E A R+PLVN+ V L + V E+ +Y+ SL A +N
Sbjct: 524 KRGNLLEPKAESARTIKLRSPLVNE-VELQAIKTGQLQVAEVSTLYDLDGVNSLEDALTN 582
Query: 574 -----VANSQAEGDGLTCLPGILSELISTGDSGSQVLSALGGTLFY-------LKKSFLD 621
+A QA + L +++ S L A+G + LK S +
Sbjct: 583 LVKTAIATVQAGAEILVLTDRPNGAILTENQSFIPPLLAVGAVHHHLIRAGLRLKASLIV 642
Query: 622 ETLLRFAKFELLPCSGFGDMAKKPYMVLDA 651
+T ++ G+G A PY+ L++
Sbjct: 643 DTAQCWSTHHFACLVGYGASAICPYLALES 672
>pdb|2WGR|A Chain A, Combining Crystallography And Molecular Dynamics: The Case
Of Schistosoma Mansoni Phospholipid Glutathione
Peroxidase
Length = 169
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 35/92 (38%), Gaps = 1/92 (1%)
Query: 773 HGCELMDQACSSLGAILENTESRQLHHILTPGKGLPAIVSILKHFKDAFDWVEANNSGRI 832
H C +++ AC S GA +N Q H GKGL + F W EA +
Sbjct: 32 HVCLIVNVACKS-GATDKNYRQLQEMHTRLVGKGLRILAFPCNQFGGQEPWAEAEIKKFV 90
Query: 833 IPHGGVDMDYDSACKKVKEIEASLTKHLKEQR 864
GV D S K L K LK ++
Sbjct: 91 TEKYGVQFDMFSKIKVNGSDADDLYKFLKSRQ 122
>pdb|2V1M|A Chain A, Crystal Structure Of Schistosoma Mansoni Glutathione
Peroxidase
Length = 169
Score = 29.6 bits (65), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 34/92 (36%), Gaps = 1/92 (1%)
Query: 773 HGCELMDQACSSLGAILENTESRQLHHILTPGKGLPAIVSILKHFKDAFDWVEANNSGRI 832
H C +++ AC GA +N Q H GKGL + F W EA +
Sbjct: 32 HVCLIVNVACKX-GATDKNYRQLQEMHTRLVGKGLRILAFPCNQFGGQEPWAEAEIKKFV 90
Query: 833 IPHGGVDMDYDSACKKVKEIEASLTKHLKEQR 864
GV D S K L K LK ++
Sbjct: 91 TEKYGVQFDMFSKIKVNGSDADDLYKFLKSRQ 122
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
0.318 0.134 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,819,730
Number of Sequences: 62578
Number of extensions: 913586
Number of successful extensions: 2152
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2091
Number of HSP's gapped (non-prelim): 36
length of query: 987
length of database: 14,973,337
effective HSP length: 108
effective length of query: 879
effective length of database: 8,214,913
effective search space: 7220908527
effective search space used: 7220908527
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)