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= psy13263
(577 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 = 112 bits (281), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 52/107 (48%), Positives = 65/107 (60%), Gaps = 7/107 (6%)
Query: 154 ETTPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQ 206
E+ SG D W H ++L + D RR P HPD++ TLYVP +FL
Sbjct: 9 ESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSC 68
Query: 207 TPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
TP M +WW IKSQNFD V+ +KVGKFYEL+HMDA+IG EL +MK
Sbjct: 69 TPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMK 115
Score = 88.6 bits (218), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 53/146 (36%), Positives = 79/146 (54%), Gaps = 5/146 (3%)
Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMS-YIEDKRN 447
RGT T DG IA +++ + I C T+F+THYHS+ + V +M+ +E++
Sbjct: 879 RGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECE 938
Query: 448 D-GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHK 506
D +TI FLYK + G CPKS+GFN A LA +PE+V++ G A + E + +LF +
Sbjct: 939 DPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLF--R 996
Query: 507 FASLVKSGEKVDVEELQKALESVKSF 532
L VD E + K L +K
Sbjct: 997 EVCLASERSTVDAEAVHKLLTLIKEL 1022
Score = 79.0 bits (193), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 42/136 (30%), Positives = 74/136 (54%), Gaps = 3/136 (2%)
Query: 252 MKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVD 311
M+E +S +L Q+ + +++ P G FPD++ L ++ AFDH++A G I PKAG D
Sbjct: 537 MEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFD 596
Query: 312 KEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQKKQKKYVLEVPSKYASKAKSN 370
+YD+ + +I+ E+ + YL Q GC T++Y + +Y LE+P + ++
Sbjct: 597 SDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGR--NRYQLEIPENFTTRNLPE 654
Query: 371 HQRVATKKKNVENYVT 386
+ + KK + Y T
Sbjct: 655 EYELKSTKKGCKRYWT 670
>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 = 68.2 bits (165), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 51/158 (32%), Positives = 81/158 (51%), Gaps = 14/158 (8%)
Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEY-MSYI----E 443
RGT T+DG IA TLE F++ + LT+F THY V + + Y M ++ E
Sbjct: 763 RGTSTHDGIAIAYATLEYFIRDVKSLTLFVTHYPPVCELEKNYSHQVGNYHMGFLVSEDE 822
Query: 444 DKRNDGI-----DTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHN 498
K + G D + FLY++ GI +S+G NVA+LA +P +++K + ++E N
Sbjct: 823 SKLDPGAAEQVPDFVTFLYQITRGIAARSYGLNVAKLADVPGEILKKAAHKSKELEGLIN 882
Query: 499 LRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQT 536
++ + FA L + ++LQK E E+QT
Sbjct: 883 TKRKRLKYFAKLWTMH---NAQDLQKWTEEFNMEETQT 917
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E +I LT+FATHY + + + VA ++ +E
Sbjct: 696 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 752
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
DTI F++ + G KS+G VA LAG+P++V+K AR LR+L
Sbjct: 753 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 795
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 206 QTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE 260
TP M Q+ +K+Q+ + +LF+++G FYELF+ DA + L S K GE
Sbjct: 9 HTPMMQQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGE 63
>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 = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E +I LT+FATHY + + + VA ++ +E
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
DTI F++ + G KS+G VA LAG+P++V+K AR LR+L
Sbjct: 754 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 32/55 (58%)
Query: 206 QTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE 260
TP M Q+ +K+Q+ + +LF+++G FY+LF+ DA + L S K GE
Sbjct: 10 HTPMMQQYLRLKAQHPEILLFYRMGDFYQLFYDDAKRASQLLDISLTKRGASAGE 64
>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 = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E +I LT+FATHY + + + VA ++ +E
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
DTI F++ + G KS+G VA LAG+P++V+K AR LR+L
Sbjct: 754 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 206 QTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE 260
TP M Q+ +K+Q+ + +LF+++G FYELF+ DA + L S K GE
Sbjct: 10 HTPMMQQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGE 64
>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 = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E +I LT+FATHY + + + VA ++ +E
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
DTI F++ + G KS+G VA LAG+P++V+K AR LR+L
Sbjct: 754 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 31/55 (56%)
Query: 206 QTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE 260
TP M Q+ +K+Q+ + +LF+++G FY LF+ DA + L S K GE
Sbjct: 10 HTPMMQQYLRLKAQHPEILLFYRMGDFYALFYDDAKRASQLLDISLTKRGASAGE 64
>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 = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E +I LT+FATHY + + + VA ++ +E
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
DTI F++ + G KS+G VA LAG+P++V+K AR LR+L
Sbjct: 754 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 31/55 (56%)
Query: 206 QTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE 260
TP M Q+ +K+Q+ + +LF+++G FY LF+ DA + L S K GE
Sbjct: 10 HTPMMQQYLRLKAQHPEILLFYRMGDFYTLFYDDAKRASQLLDISLTKRGASAGE 64
>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 = 5e-09, Method: Compositional matrix adjust.
Identities = 40/114 (35%), Positives = 57/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E +I LT+FATHY + + + VA ++ +E
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKXEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
DTI F + + G KS+G VA LAG+P++V+K AR LR+L
Sbjct: 754 --DTIAFXHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 201 EFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE 260
E TP Q+ +K+Q+ + +LF++ G FYELF+ DA + L S K GE
Sbjct: 5 ENFDAHTPXXQQYLRLKAQHPEILLFYRXGDFYELFYDDAKRASQLLDISLTKRGASAGE 64
>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 = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 39/113 (34%), Positives = 57/113 (50%), Gaps = 15/113 (13%)
Query: 391 GTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
GT T DG +A E +I LT+FATHY + + + VA ++ +E
Sbjct: 698 GTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG---- 753
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
DTI F++ + G KS+G VA LAG+P++V+K AR LR+L
Sbjct: 754 -DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 206 QTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE 260
TP M Q+ +K+Q+ + +LF+++G FYELF+ DA + L S K GE
Sbjct: 10 HTPMMQQYLRLKAQHPEILLFYRMGDFYELFYDDAKRASQLLDISLTKRGASAGE 64
>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH
ADP BOUND TO Msh2 Only
Length = 934
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 34/106 (32%), Positives = 54/106 (50%), Gaps = 6/106 (5%)
Query: 390 RGTGTNDGCVIARVTLEKF-LQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E +IG +FATH+H + + P V + +
Sbjct: 752 RGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTV-----NNLHVTALT 806
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
+T+ LY++ G+C +SFG +VAELA P+ V++ A ++E
Sbjct: 807 TEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELE 852
>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 = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 34/106 (32%), Positives = 54/106 (50%), Gaps = 6/106 (5%)
Query: 390 RGTGTNDGCVIARVTLEKF-LQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E +IG +FATH+H + + P V + +
Sbjct: 752 RGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTV-----NNLHVTALT 806
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
+T+ LY++ G+C +SFG +VAELA P+ V++ A ++E
Sbjct: 807 TEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELE 852
>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 = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 50/107 (46%), Gaps = 7/107 (6%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
RGT + DG IA E + T+FATHY + + + + +
Sbjct: 666 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELT-------ALGLPRLKNLHVAAREE 718
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR 496
+VF ++++PG KS+G VA +AG+P++VV + M AR
Sbjct: 719 AGGLVFYHQVLPGPASKSYGVEVAAMAGLPKEVVARARALLQAMAAR 765
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 208 PCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDA 240
P + Q+ ++ Q D +L F+VG FYE F DA
Sbjct: 15 PLLQQYVELRDQYPDYLLLFQVGDFYECFGEDA 47
>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 = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
RGT + DG IA E + T+FATHY + + + + +
Sbjct: 666 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELT-------ALGLPRLKNLHVAAREE 718
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVV 483
+VF ++++PG KS+G VA AG+P++VV
Sbjct: 719 AGGLVFYHQVLPGPASKSYGVEVAAXAGLPKEVV 752
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 208 PCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDA 240
P + Q+ ++ Q D +L F+VG FYE F DA
Sbjct: 15 PLLQQYVELRDQYPDYLLLFQVGDFYECFGEDA 47
>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts
pdb|1EWR|B Chain B, Crystal Structure Of Taq Muts
Length = 649
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
RGT + DG IA E + T+FATHY + + + + +
Sbjct: 550 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELT-------ALGLPRLKNLHVAAREE 602
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVV 483
+VF ++++PG KS+G VA AG+P++VV
Sbjct: 603 AGGLVFYHQVLPGPASKSYGVEVAAXAGLPKEVV 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 = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
RGT + DG IA E + T+FATHY + + + + +
Sbjct: 666 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELT-------ALGLPRLKNLHVAAREE 718
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVV 483
+VF ++++PG KS+G VA AG+P++VV
Sbjct: 719 AGGLVFYHQVLPGPASKSYGVEVAAXAGLPKEVV 752
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 208 PCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDA 240
P + Q+ ++ Q D +L F+VG FYE F DA
Sbjct: 15 PLLQQYVELRDQYPDYLLLFQVGDFYECFGEDA 47
>pdb|3BIP|A Chain A, Crystal Structure Of Yeast Spt16 N-Terminal Domain
pdb|3BIP|B Chain B, Crystal Structure Of Yeast Spt16 N-Terminal Domain
pdb|3BIQ|A Chain A, Crystal Structure Of Yeast Spt16 N-Terminal Domain
Length = 467
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 442 IEDKRNDGIDTIVFLYKLVP---GICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHN 498
+ DK + ID + FL +L P +CP ++ FN L +++ G ++ AR
Sbjct: 219 LSDKIENKIDDVKFLKQLSPDLSALCPPNYKFNFDLLDWTYSPIIQSGKKFDLRVSARST 278
Query: 499 LRQLF 503
QL+
Sbjct: 279 NDQLY 283
>pdb|3BIT|A Chain A, Crystal Structure Of Yeast Spt16 N-Terminal Domain
pdb|3BIT|B Chain B, Crystal Structure Of Yeast Spt16 N-Terminal Domain
Length = 453
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 442 IEDKRNDGIDTIVFLYKLVP---GICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHN 498
+ DK + ID + FL +L P +CP ++ FN L +++ G ++ AR
Sbjct: 219 LSDKIENKIDDVKFLKQLSPDLSALCPPNYKFNFDLLDWTYSPIIQSGKKFDLRVSARST 278
Query: 499 LRQLF 503
QL+
Sbjct: 279 NDQLY 283
>pdb|3K53|A Chain A, Crystal Structure Of Nfeob From P. Furiosus
pdb|3K53|B Chain B, Crystal Structure Of Nfeob From P. Furiosus
pdb|3K53|C Chain C, Crystal Structure Of Nfeob From P. Furiosus
pdb|3K53|D Chain D, Crystal Structure Of Nfeob From P. Furiosus
Length = 271
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 27/42 (64%), Gaps = 2/42 (4%)
Query: 485 FGTTVAFQMEARHNLRQLFIHKFASLVKSGEKVDVEELQKAL 526
F T F+ME ++ + L ++KF L K G K+D+++++K L
Sbjct: 99 FLTLELFEMEVKNII--LVLNKFDLLKKKGAKIDIKKMRKEL 138
>pdb|1ACO|A Chain A, Crystal Structure Of Aconitase With Transaconitate Bound
pdb|1FGH|A Chain A, Complex With 4-Hydroxy-Trans-Aconitate
pdb|8ACN|A Chain A, Crystal Structures Of Aconitase With Isocitrate And
Nitroisocitrate Bound
Length = 754
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 513 SGEKVDVEELQKALESVKSFESQTKKDLEDL 543
SG++VDV + L+ ++ F+ KDLEDL
Sbjct: 525 SGQRVDVSPTSQRLQLLEPFDKWDGKDLEDL 555
>pdb|1B0M|A Chain A, Aconitase R644q:fluorocitrate Complex
Length = 753
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 513 SGEKVDVEELQKALESVKSFESQTKKDLEDL 543
SG++VDV + L+ ++ F+ KDLEDL
Sbjct: 524 SGQRVDVSPTSQRLQLLEPFDKWDGKDLEDL 554
>pdb|1C97|A Chain A, S642a:isocitrate Complex Of Aconitase
pdb|1B0K|A Chain A, S642a:fluorocitrate Complex Of Aconitase
Length = 753
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 513 SGEKVDVEELQKALESVKSFESQTKKDLEDL 543
SG++VDV + L+ ++ F+ KDLEDL
Sbjct: 524 SGQRVDVSPTSQRLQLLEPFDKWDGKDLEDL 554
>pdb|5ACN|A Chain A, Structure Of Activated Aconitase. Formation Of The
(4fe-4s) Cluster In The Crystal
pdb|6ACN|A Chain A, Structure Of Activated Aconitase. Formation Of The
(4fe-4s) Cluster In The Crystal
pdb|7ACN|A Chain A, Crystal Structures Of Aconitase With Isocitrate And
Nitroisocitrate Bound
Length = 754
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 513 SGEKVDVEELQKALESVKSFESQTKKDLEDL 543
SG++VDV + L+ ++ F+ KDLEDL
Sbjct: 525 SGQRVDVSPTSQRLQLLEPFDKWDGKDLEDL 555
>pdb|1B0J|A Chain A, Crystal Structure Of Aconitase With Isocitrate
Length = 754
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 513 SGEKVDVEELQKALESVKSFESQTKKDLEDL 543
SG++VDV + L+ ++ F+ KDLEDL
Sbjct: 525 SGQRVDVSPTSQRLQLLEPFDKWDGKDLEDL 555
>pdb|1NIS|A Chain A, Crystal Structure Of Aconitase With Trans-Aconitate And
Nitrocitrate Bound
pdb|1NIT|A Chain A, Crystal Structure Of Aconitase With Trans-Aconitate And
Nitrocitrate Bound
Length = 754
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 513 SGEKVDVEELQKALESVKSFESQTKKDLEDL 543
SG++VDV + L+ ++ F+ KDLEDL
Sbjct: 525 SGQRVDVSPTSQRLQLLEPFDKWDGKDLEDL 555
>pdb|1AMI|A Chain A, Steric And Conformational Features Of The Aconitase
Mechanism
pdb|1AMJ|A Chain A, Steric And Conformational Features Of The Aconitase
Mechanism
Length = 754
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 513 SGEKVDVEELQKALESVKSFESQTKKDLEDL 543
SG++VDV + L+ ++ F+ KDLEDL
Sbjct: 525 SGQRVDVSPTSQRLQLLEPFDKWDGKDLEDL 555
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
0.312 0.129 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,592,805
Number of Sequences: 62578
Number of extensions: 661319
Number of successful extensions: 1266
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1217
Number of HSP's gapped (non-prelim): 39
length of query: 577
length of database: 14,973,337
effective HSP length: 104
effective length of query: 473
effective length of database: 8,465,225
effective search space: 4004051425
effective search space used: 4004051425
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)