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= psy13355
(314 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3QSB|B Chain B, Structure Of E. Coli Poliiibeta With
(Z)-5-(1-((4'-Fluorobiphenyl-4-
Yl)methoxyimino)butyl)-2,2-Dimethyl-4,
6-Dioxocyclohexanecarbonitrile
Length = 366
Score = 206 bits (525), Expect = 9e-54, Method: Compositional matrix adjust.
Identities = 103/299 (34%), Positives = 169/299 (56%), Gaps = 2/299 (0%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKA 306
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGXDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEA 302
>pdb|3Q4L|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4L|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
Length = 368
Score = 206 bits (523), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 103/299 (34%), Positives = 169/299 (56%), Gaps = 2/299 (0%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 8 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 67
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 68 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 126
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 127 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 186
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 187 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 245
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKA 306
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 246 YRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEA 304
>pdb|2POL|A Chain A, Three-Dimensional Structure Of The Beta Subunit Of
Escherichia Coli Dna Polymerase Iii Holoenzyme: A
Sliding Dna Clamp
pdb|2POL|B Chain B, Three-Dimensional Structure Of The Beta Subunit Of
Escherichia Coli Dna Polymerase Iii Holoenzyme: A
Sliding Dna Clamp
pdb|1MMI|A Chain A, E. Coli Dna Polymerase Beta Subunit
pdb|1MMI|B Chain B, E. Coli Dna Polymerase Beta Subunit
pdb|1UNN|A Chain A, Complex Of Beta-Clamp Processivity Factor And Little
Finger Domain Of Poliv
pdb|1UNN|B Chain B, Complex Of Beta-Clamp Processivity Factor And Little
Finger Domain Of Poliv
pdb|1OK7|A Chain A, A Conserved Protein Binding-site On Bacterial Sliding
Clamps
pdb|1OK7|B Chain B, A Conserved Protein Binding-site On Bacterial Sliding
Clamps
pdb|3BEP|A Chain A, Structure Of A Sliding Clamp On Dna
pdb|3BEP|B Chain B, Structure Of A Sliding Clamp On Dna
pdb|3D1E|A Chain A, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound To
A Polymerase Ii Peptide
pdb|3D1E|B Chain B, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound To
A Polymerase Ii Peptide
pdb|3D1F|A Chain A, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound To
A Polymerase Iii Peptide
pdb|3D1F|B Chain B, Crystal Structure Of E. Coli Sliding Clamp (Beta) Bound To
A Polymerase Iii Peptide
pdb|3D1G|A Chain A, Structure Of A Small Molecule Inhibitor Bound To A Dna
Sliding Clamp
pdb|3D1G|B Chain B, Structure Of A Small Molecule Inhibitor Bound To A Dna
Sliding Clamp
pdb|3QSB|A Chain A, Structure Of E. Coli Poliiibeta With
(Z)-5-(1-((4'-Fluorobiphenyl-4-
Yl)methoxyimino)butyl)-2,2-Dimethyl-4,
6-Dioxocyclohexanecarbonitrile
pdb|3Q4J|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|C Chain C, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|D Chain D, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|E Chain E, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4J|F Chain F, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4K|A Chain A, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
pdb|3Q4K|B Chain B, Structure Of A Small Peptide Ligand Bound To E.Coli Dna
Sliding Clamp
Length = 366
Score = 206 bits (523), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 103/299 (34%), Positives = 169/299 (56%), Gaps = 2/299 (0%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKA 306
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEA 302
>pdb|3PWE|A Chain A, Crystal Structure Of The E. Coli Beta Clamp Mutant R103c,
I305c, C260s, C333s At 2.2a Resolution
pdb|3PWE|B Chain B, Crystal Structure Of The E. Coli Beta Clamp Mutant R103c,
I305c, C260s, C333s At 2.2a Resolution
Length = 366
Score = 205 bits (521), Expect = 3e-53, Method: Compositional matrix adjust.
Identities = 105/307 (34%), Positives = 171/307 (55%), Gaps = 3/307 (0%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGCSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKAS 307
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGSDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAE 303
Query: 308 ST-DLIY 313
D+ Y
Sbjct: 304 ECLDVTY 310
>pdb|2XUR|A Chain A, The G157c Mutation In The Escherichia Coli Sliding Clamp
Specifically Affects Initiation Of Replication
pdb|2XUR|B Chain B, The G157c Mutation In The Escherichia Coli Sliding Clamp
Specifically Affects Initiation Of Replication
Length = 373
Score = 202 bits (513), Expect = 3e-52, Method: Compositional matrix adjust.
Identities = 102/299 (34%), Positives = 168/299 (56%), Gaps = 2/299 (0%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 13 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 72
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 73 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 131
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLN +L + + + V++DGHRL + I
Sbjct: 132 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNCMLFETEGEELRTVATDGHRLAVCSMPI 191
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 192 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 250
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKA 306
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 251 YRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEA 309
>pdb|1JQL|A Chain A, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of Beta-Delta (1-140)
pdb|1JQJ|A Chain A, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of The Beta-Delta Complex
pdb|1JQJ|B Chain B, Mechanism Of Processivity Clamp Opening By The Delta
Subunit Wrench Of The Clamp Loader Complex Of E. Coli
Dna Polymerase Iii: Structure Of The Beta-Delta Complex
Length = 366
Score = 197 bits (501), Expect = 7e-51, Method: Compositional matrix adjust.
Identities = 102/299 (34%), Positives = 167/299 (55%), Gaps = 2/299 (0%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKA 306
Y+ V+ +K + L ++ R + SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGCDLLKQAFARAAAASNEKFRGVRLYVSENQLKITANNPEQEEA 302
>pdb|3F1V|A Chain A, E. Coli Beta Sliding Clamp, 148-153 Ala Mutant
pdb|3F1V|B Chain B, E. Coli Beta Sliding Clamp, 148-153 Ala Mutant
Length = 366
Score = 192 bits (489), Expect = 1e-49, Method: Compositional matrix adjust.
Identities = 100/299 (33%), Positives = 165/299 (55%), Gaps = 2/299 (0%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSS 67
E+ +L PLQ V + + LPIL N+L+ +S TD E+++ A+ +
Sbjct: 6 EREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEP 65
Query: 68 INIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKY 127
V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P + + +
Sbjct: 66 GATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD-DWQS 124
Query: 128 DFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNI 187
+ EFTL Q T+K ++ FS+A YYLNG+L + + + V++DGHRL + I
Sbjct: 125 EVEFTLPQATMKRLIEATQFSMAAAAAAYYLNGMLFETEGEELRTVATDGHRLAVCSMPI 184
Query: 188 DKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKFLD 247
+ S S +I+PRK V L R+L+ +NP+ ++I +N DG+F D
Sbjct: 185 GQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPD 243
Query: 248 YKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSNREKA 306
Y+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++ +E+A
Sbjct: 244 YRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEA 302
>pdb|2AWA|A Chain A, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec
2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae
Tigr4 At 2.50 A Resolution
pdb|2AWA|B Chain B, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec
2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae
Tigr4 At 2.50 A Resolution
pdb|2AWA|C Chain C, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec
2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae
Tigr4 At 2.50 A Resolution
pdb|2AWA|D Chain D, Crystal Structure Of Dna Polymerase Iii, Beta Chain (Ec
2.7.7.7) (Np_344555.1) From Streptococcus Pneumoniae
Tigr4 At 2.50 A Resolution
Length = 390
Score = 88.2 bits (217), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 77/302 (25%), Positives = 145/302 (48%), Gaps = 14/302 (4%)
Query: 9 KNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSI 68
KN L L + KN +PILS + + +E I+ + ++ ++ I + + ++ +
Sbjct: 20 KNLFLQALNTTKRAISSKNAIPILSTVKIDVTNEGITLIGSNGQISIENFISQKNEDAGL 79
Query: 69 ------NIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYP-IM 121
+I++ A FI+++ SLP+ IE + + SGKS+ TL+ D+++YP I
Sbjct: 80 LITSLGSILLEASFFINVVSSLPDVTLDFKEIEQNQIVLTSGKSEITLKGKDSEQYPRIQ 139
Query: 122 TLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGL--LLSFQKKNIIAVSSDGHR 179
+++ L K LK I+N F+ + Q+ R L G+ +LS Q K + V++D HR
Sbjct: 140 EISAST--PLILETKLLKKIINETAFAASTQESRPILTGVHFVLS-QHKELKTVATDSHR 196
Query: 180 LTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXX 239
L+ ++ ++K S D++IP +++ + + VE+ +NNQ
Sbjct: 197 LSQKKLTLEKN-SDDFDVVIPSRSLREFSAVFTDDIETVEIFFANNQILFRSENISFYTR 255
Query: 240 XXDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG-VRLVIKPNYLKITV 298
+G + D +I + + N L +S +R ++S+ G V+L IK + V
Sbjct: 256 LLEGNYPDTDRLIPTDFNTTITFNVVNLRQSXERARLLSSATQNGTVKLEIKDGVVSAHV 315
Query: 299 SS 300
S
Sbjct: 316 HS 317
>pdb|2AVT|A Chain A, Crystal Structure Of The Beta Subunit From Dna Polymerase
Of Streptococcus Pyogenes
pdb|2AVT|B Chain B, Crystal Structure Of The Beta Subunit From Dna Polymerase
Of Streptococcus Pyogenes
Length = 378
Score = 83.2 bits (204), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 73/296 (24%), Positives = 136/296 (45%), Gaps = 10/296 (3%)
Query: 13 LHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSI---- 68
+H L + KN +PILS+I + S ++ ++ ++ I V N+ +
Sbjct: 12 IHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIPVSNENAGLLITS 71
Query: 69 --NIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSK 126
I++ A FI+I+ SLP+ IE + + SGKS+ TL+ D +YP + S
Sbjct: 72 PGAILLEASFFINIISSLPDISINVKEIEQHQVVLTSGKSEITLKGKDVDQYPRLQEVST 131
Query: 127 YDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQ-KKNIIAVSSDGHRLTYYQV 185
+ L K LK I+ F+ + Q+ R L G+ + K+ AV++D HR++ +
Sbjct: 132 EN-PLILKTKLLKSIIAETAFAASLQESRPILTGVHIVLSNHKDFKAVATDSHRMSQRLI 190
Query: 186 NIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQXXXXXXXXXXXXXXXDGKF 245
+D S+ +++P K++ + + VE+ S +Q +G +
Sbjct: 191 TLDNT-SADFMVVLPSKSLREFSAVFTDDIETVEVFFSPSQILFRSEHISFYTRLLEGNY 249
Query: 246 LDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG-VRLVIKPNYLKITVSS 300
D ++ ++E + N L +++R +ISN G V+L I N++ V+S
Sbjct: 250 PDTDRLLMTEFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQNHISAHVNS 305
>pdb|1VPK|A Chain A, Crystal Structure Of Dna Polymerase Iii, Beta Subunit
(Tm0262) From Thermotoga Maritima At 2.00 A Resolution
Length = 378
Score = 77.8 bits (190), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 61/279 (21%), Positives = 124/279 (44%), Gaps = 5/279 (1%)
Query: 25 KKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDILRSL 84
KK++ PIL+ L +TD E + + +V +++ L
Sbjct: 35 KKSVKPILAGFLFEVKDGNFYICATDLETGVKATVNAAEISGEARFVVPGDVIQKMVKVL 94
Query: 85 PETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCILNM 144
P+ E + +E + I SG + F + T+ A E+P +T ++ F + L+ ++
Sbjct: 95 PD-EITELSLEGDALVISSGSTVFRITTMPADEFPEIT-PAESGITFEVDTSLLEEMVEK 152
Query: 145 VYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSDIIIPRKTV 204
V F+ A+ + LNG+ K + V+SDG RL + + + ++ K++
Sbjct: 153 VIFAAAKDEFMRNLNGVFWELHKNLLRLVASDGFRLALAEEQ--IENEEEASFLLSLKSM 210
Query: 205 FTLQRLLENKENP-VELKISNNQXXXXXXXXXXXXXXXDGKFLDYKYVISNKYEKSFLVN 263
+Q +L+N P + ++ + D +F DYK VI ++ +V+
Sbjct: 211 KEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETVMRVVDAEFPDYKRVIPETFKTKVVVS 270
Query: 264 RNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSSN 302
R +L SL+R+ +I++ + V+ I+ N +++ S +
Sbjct: 271 RKELRESLKRVMVIASKGSESVKFEIEENVMRLVSKSPD 309
>pdb|3T0P|A Chain A, Crystal Structure Of A Putative Dna Polymerase Iii Beta
Subunit (Eubrec_0002; Ere_29750) From Eubacterium
Rectale Atcc 33656 At 2.26 A Resolution
pdb|3T0P|B Chain B, Crystal Structure Of A Putative Dna Polymerase Iii Beta
Subunit (Eubrec_0002; Ere_29750) From Eubacterium
Rectale Atcc 33656 At 2.26 A Resolution
Length = 371
Score = 65.1 bits (157), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 64/276 (23%), Positives = 119/276 (43%), Gaps = 16/276 (5%)
Query: 9 KNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSI 68
K +L + +V V + IL IL+ ++ +I + D E+ I T I
Sbjct: 8 KANLLKGVNIVSKAVPTRTTXAILECILIDASANEIKLXANDXELGIETIIDGTIEERGI 67
Query: 69 NIIVAARKFIDILRSLPETEKVTIYIENKHMF---IKSGKSKFTLQTLDAKEY---PIMT 122
I + A+ F +I+R LP+ + + IE F I K+KF + ++ P +
Sbjct: 68 -IALDAKIFSEIVRKLPDND---VTIETDASFKTVISCEKAKFNIIGKSGDDFSYIPYVE 123
Query: 123 LNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTY 182
N LSQ TLK ++ FSIA D G L ++ + VS DGHR++
Sbjct: 124 RNES----IVLSQFTLKEVIRQTIFSIADNDNNKLXTGELFEIEENKLRVVSLDGHRISI 179
Query: 183 YQVNIDKKFSSCSDIIIPRKTVFTLQRLLEN-KENPVELKISNNQXXXXXXXXXXXXXXX 241
+ + S +++P KT+ + +++ + V + I+NN
Sbjct: 180 RYIEXKNHYDS-KKVVVPGKTLQEISKIIPGSADEDVVIYITNNHIVFEFENTTVVSRLI 238
Query: 242 DGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISII 277
+G++ +S+ Y+ +N+ +LL + R +++
Sbjct: 239 EGEYFKIDQXLSSDYDTKVRINKRELLDCIDRATLL 274
>pdb|3P16|A Chain A, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|B Chain B, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|C Chain C, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|D Chain D, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|E Chain E, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|F Chain F, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
Length = 408
Score = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 39/187 (20%), Positives = 87/187 (46%), Gaps = 13/187 (6%)
Query: 23 VEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDILR 82
+ + +P+LS +L+ + ++ D EV S +++V+ R DI R
Sbjct: 39 LPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEI-VSPGSVLVSGRLLSDITR 97
Query: 83 SLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCIL 142
+LP + V +++E + + G ++F+L T+ ++YP TL + + L + +
Sbjct: 98 ALP-NKPVDVHVEGNRVALTCGNARFSLPTMPVEDYP--TLPTLPEETGLLPAELFAEAI 154
Query: 143 NMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSD-----I 197
+ V + + D L G+ + + ++ ++D RL ++ K+S+ S +
Sbjct: 155 SQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVREL----KWSASSPDIEAAV 210
Query: 198 IIPRKTV 204
++P KT+
Sbjct: 211 LVPAKTL 217
>pdb|3RB9|A Chain A, Crystal Structure Of The M. Tuberculosis Beta Clamp
pdb|3RB9|B Chain B, Crystal Structure Of The M. Tuberculosis Beta Clamp
Length = 395
Score = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 39/187 (20%), Positives = 87/187 (46%), Gaps = 13/187 (6%)
Query: 23 VEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDILR 82
+ + +P+LS +L+ + ++ D EV S +++V+ R DI R
Sbjct: 26 LPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEI-VSPGSVLVSGRLLSDITR 84
Query: 83 SLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTLKCIL 142
+LP + V +++E + + G ++F+L T+ ++YP TL + + L + +
Sbjct: 85 ALP-NKPVDVHVEGNRVALTCGNARFSLPTMPVEDYP--TLPTLPEETGLLPAELFAEAI 141
Query: 143 NMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSCSD-----I 197
+ V + + D L G+ + + ++ ++D RL ++ K+S+ S +
Sbjct: 142 SQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVREL----KWSASSPDIEAAV 197
Query: 198 IIPRKTV 204
++P KT+
Sbjct: 198 LVPAKTL 204
>pdb|2Y69|D Chain D, Bovine Heart Cytochrome C Oxidase Re-Refined With
Molecular Oxygen
pdb|2Y69|Q Chain Q, Bovine Heart Cytochrome C Oxidase Re-Refined With
Molecular Oxygen
Length = 169
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 31/66 (46%)
Query: 65 NSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLN 124
N ++ AA FI L EK +Y H F + +K T + LD K PI +
Sbjct: 98 NEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFS 157
Query: 125 SKYDFE 130
+K+D++
Sbjct: 158 AKWDYD 163
>pdb|1OCC|D Chain D, Structure Of Bovine Heart Cytochrome C Oxidase At The
Fully Oxidized State
pdb|1OCC|Q Chain Q, Structure Of Bovine Heart Cytochrome C Oxidase At The
Fully Oxidized State
pdb|2OCC|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2OCC|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1OCO|D Chain D, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
State
pdb|1OCO|Q Chain Q, Bovine Heart Cytochrome C Oxidase In Carbon Monoxide-bound
State
pdb|1OCR|D Chain D, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|1OCR|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|1OCZ|D Chain D, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
pdb|1OCZ|Q Chain Q, Bovine Heart Cytochrome C Oxidase In Azide-Bound State
pdb|1V54|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1V54|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|1V55|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
State
pdb|1V55|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Reduced
State
pdb|2DYR|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2DYR|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State
pdb|2DYS|D Chain D, Bovine Heart Cytochrome C Oxidase Modified By Dccd
pdb|2DYS|Q Chain Q, Bovine Heart Cytochrome C Oxidase Modified By Dccd
pdb|2EIJ|D Chain D, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|2EIJ|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Fully Reduced
State
pdb|2EIK|D Chain D, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIK|Q Chain Q, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIL|D Chain D, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2EIL|Q Chain Q, Cadmium Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2EIM|D Chain D, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIM|Q Chain Q, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Reduced State
pdb|2EIN|D Chain D, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2EIN|Q Chain Q, Zinc Ion Binding Structure Of Bovine Heart Cytochrome C
Oxidase In The Fully Oxidized State
pdb|2ZXW|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (1-S X-Ray Exposure Dataset)
pdb|2ZXW|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (1-S X-Ray Exposure Dataset)
pdb|3ABL|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (15-S X-Ray Exposure Dataset)
pdb|3ABL|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (15-S X-Ray Exposure Dataset)
pdb|3ABM|D Chain D, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (200-S X-Ray Exposure Dataset)
pdb|3ABM|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The Fully Oxidized
State (200-S X-Ray Exposure Dataset)
pdb|3ABK|D Chain D, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
Reduced State (50k)
pdb|3ABK|Q Chain Q, Bovine Heart Cytochrome C Oxidase At The No-Bound Fully
Reduced State (50k)
pdb|3AG1|D Chain D, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 280 K
pdb|3AG1|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 280 K
pdb|3AG2|D Chain D, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 100 K
pdb|3AG2|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Carbon
Monoxide-Bou Reduced State At 100 K
pdb|3AG3|D Chain D, Bovine Heart Cytochrome C Oxidase In The Nitric
Oxide-Bound Reduced State At 100 K
pdb|3AG3|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Nitric
Oxide-Bound Reduced State At 100 K
pdb|3AG4|D Chain D, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
F Reduced State At 100 K
pdb|3AG4|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Cyanide Ion-Bound
F Reduced State At 100 K
pdb|3ASN|D Chain D, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 1.7470 Angstrom Wavelength
pdb|3ASN|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 1.7470 Angstrom Wavelength
pdb|3ASO|D Chain D, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 0.9 Angstrom Wavelength
pdb|3ASO|Q Chain Q, Bovine Heart Cytochrome C Oxidase In The Fully Oxidized
State Measured At 0.9 Angstrom Wavelength
pdb|2YBB|O Chain O, Fitted Model For Bovine Mitochondrial Supercomplex
I1iii2iv1 By Single Particle Cryo-Em (Emd-1876)
Length = 147
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 9/103 (8%)
Query: 37 VCKNSEKISFLSTDTEVQITTY-----TAVGYGNSSIN----IIVAARKFIDILRSLPET 87
K EK S+ S + ++ Y + N S N ++ AA FI L
Sbjct: 39 ALKEKEKASWSSLSIDEKVELYRLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIW 98
Query: 88 EKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFE 130
EK +Y H F + +K T + LD K PI ++K+D++
Sbjct: 99 EKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYD 141
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
0.319 0.134 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,631,692
Number of Sequences: 62578
Number of extensions: 271543
Number of successful extensions: 776
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 738
Number of HSP's gapped (non-prelim): 15
length of query: 314
length of database: 14,973,337
effective HSP length: 99
effective length of query: 215
effective length of database: 8,778,115
effective search space: 1887294725
effective search space used: 1887294725
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)