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= 002972
(862 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 72/327 (22%), Positives = 127/327 (38%), Gaps = 24/327 (7%)
Query: 183 ILIVGLSGIGKSCLARQVASDPPERFVGGAVELGFGQWCSRAACNGSKSDYQKRLARKIS 242
+ I G++G GKS LA + D + G G W S KS +L +
Sbjct: 150 VTIHGMAGCGKSVLAAEAVRD--HSLLEGCFPGGV-HWVSVG--KQDKSGLLMKLQNLCT 204
Query: 243 KFLVQIGFWKKIKDENSDLEYLCCLLQEALYGKSILILLDDVWEQDIVERFAKLYDNDCK 302
+ F +++ + + +L + +S+LIL DDVW+ ++ K +D+ C+
Sbjct: 205 RLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLIL-DDVWDSWVL----KAFDSQCQ 259
Query: 303 YLVTTRNEAVYEITEAEKVELSKDDIMEISKS--ILLYHXXXXXXXXXXXXXXXXXRCGH 360
L+TTR+++V + K + + + K IL C
Sbjct: 260 ILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKG 319
Query: 361 HPLTVAVMGKALRKELRSEKWEKAITDLSTFATCAPGPVSYVNEKEAENTLTIFGSFEFS 420
PL V+++G LR +WE + L S + + + ++I S
Sbjct: 320 SPLVVSLIGALLRD--FPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSI------S 371
Query: 421 LEAMPRDSRRLFIALAALSWAEPVPEACLEAIWSILVQKSLFSLAVCKLVEGSLLMKDDT 480
+E + D + + L+ L VP L +W + ++ L + V SLL D
Sbjct: 372 VEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQ--EFVNKSLLFCDRN 429
Query: 481 DP--LYQVHDMVSLYLDSKTNDSIQML 505
Y +HD+ +L K +Q L
Sbjct: 430 GKSFRYYLHDLQVDFLTEKNCSQLQDL 456
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 37.7 bits (86), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 70/330 (21%), Positives = 126/330 (38%), Gaps = 30/330 (9%)
Query: 183 ILIVGLSGIGKSCLARQVASDPP---ERFVGGAVELGFGQWCSRAACNGSKSDYQKRLAR 239
+ I G++G GKS LA + D F GG + G+ KS +L
Sbjct: 150 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK--------QDKSGLLMKLQN 201
Query: 240 KISKFLVQIGFWKKIKDENSDLEYLCCLLQEALYGKSILILLDDVWEQDIVERFAKLYDN 299
+ + F +++ + + +L + +S+LIL DDVW+ ++ K +DN
Sbjct: 202 LCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLIL-DDVWDPWVL----KAFDN 256
Query: 300 DCKYLVTTRNEAVYEITEAEK--VELSKDDIMEISKSILLYHXXXXXXXXXXXXXXXXXR 357
C+ L+TTR+++V + K V + E IL
Sbjct: 257 QCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKE 316
Query: 358 CGHHPLTVAVMGKALRKELRSEKWEKAITDLSTFATCAPGPVSYVNEKEAENTLTIFGSF 417
C PL V+++G LR +W + L + + + + + +
Sbjct: 317 CKGSPLVVSLIGALLRD--FPNRWAYYLRQLQN------KQFKRIRKSSSYDYEALDEAM 368
Query: 418 EFSLEAMPRDSRRLFIALAALSWAEPVPEACLEAIWSILVQKSLFSLAVCKLVEGSLLM- 476
S+E + D + + L+ L VP L +W + ++ L + V SLL
Sbjct: 369 SISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVEDILQ--EFVNKSLLFC 426
Query: 477 -KDDTDPLYQVHDMVSLYLDSKTNDSIQML 505
++ Y +HD+ +L K +Q L
Sbjct: 427 NRNGKSFCYYLHDLQVDFLTEKNRSQLQDL 456
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 37.7 bits (86), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 70/330 (21%), Positives = 127/330 (38%), Gaps = 30/330 (9%)
Query: 183 ILIVGLSGIGKSCLARQVASDPP---ERFVGGAVELGFGQWCSRAACNGSKSDYQKRLAR 239
+ I G++G GKS LA + D F GG + G+ KS +L
Sbjct: 156 VTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGK--------QDKSGLLMKLQN 207
Query: 240 KISKFLVQIGFWKKIKDENSDLEYLCCLLQEALYGKSILILLDDVWEQDIVERFAKLYDN 299
++ F +++ + + +L + +S+LIL DDVW+ ++ K +D+
Sbjct: 208 LCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLIL-DDVWDSWVL----KAFDS 262
Query: 300 DCKYLVTTRNEAVYEITEAEKVELSKDDIMEISKS--ILLYHXXXXXXXXXXXXXXXXXR 357
C+ L+TTR+++V + K + + + K IL
Sbjct: 263 QCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKE 322
Query: 358 CGHHPLTVAVMGKALRKELRSEKWEKAITDLSTFATCAPGPVSYVNEKEAENTLTIFGSF 417
C PL V+++G LR +WE + L + + + + + +
Sbjct: 323 CKGSPLVVSLIGALLRD--FPNRWEYYLKQLQN------KQFKRIRKSSSYDYEALDEAM 374
Query: 418 EFSLEAMPRDSRRLFIALAALSWAEPVPEACLEAIWSILVQKSLFSLAVCKLVEGSLLMK 477
S+E + D + + L+ L VP L +W + ++ L + V SLL
Sbjct: 375 SISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQ--EFVNKSLLFC 432
Query: 478 DDTDP--LYQVHDMVSLYLDSKTNDSIQML 505
D Y +HD+ +L K +Q L
Sbjct: 433 DRNGKSFRYYLHDLQVDFLTEKNCSQLQDL 462
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 69/330 (20%), Positives = 125/330 (37%), Gaps = 30/330 (9%)
Query: 183 ILIVGLSGIGKSCLARQVASDPP---ERFVGGAVELGFGQWCSRAACNGSKSDYQKRLAR 239
+ I G++G GKS LA + D F GG + G+ KS +L
Sbjct: 157 VTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK--------QDKSGLLMKLQN 208
Query: 240 KISKFLVQIGFWKKIKDENSDLEYLCCLLQEALYGKSILILLDDVWEQDIVERFAKLYDN 299
+ + F +++ + + +L + +S+LIL DDVW+ ++ K +DN
Sbjct: 209 LCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLIL-DDVWDPWVL----KAFDN 263
Query: 300 DCKYLVTTRNEAVYEITEAEK--VELSKDDIMEISKSILLYHXXXXXXXXXXXXXXXXXR 357
C+ L+TT +++V + K V + E IL
Sbjct: 264 QCQILLTTSDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKE 323
Query: 358 CGHHPLTVAVMGKALRKELRSEKWEKAITDLSTFATCAPGPVSYVNEKEAENTLTIFGSF 417
C PL V+++G LR +W + L + + + + + +
Sbjct: 324 CKGSPLVVSLIGALLRD--FPNRWAYYLRQLQN------KQFKRIRKSSSYDYEALDEAM 375
Query: 418 EFSLEAMPRDSRRLFIALAALSWAEPVPEACLEAIWSILVQKSLFSLAVCKLVEGSLLM- 476
S+E + D + + L+ L VP L +W + ++ L + V SLL
Sbjct: 376 SISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVEDILQ--EFVNKSLLFC 433
Query: 477 -KDDTDPLYQVHDMVSLYLDSKTNDSIQML 505
++ Y +HD+ +L K +Q L
Sbjct: 434 NRNGKSFCYYLHDLQVDFLTEKNRSQLQDL 463
>pdb|1C72|A Chain A, Tyr115, Gln165 And Trp209 Contribute To The
1,2-Epoxy-3-(P- Nitrophenoxy)propane Conjugating
Activities Of Glutathione S-Transferase Cgstm1-1
pdb|1C72|B Chain B, Tyr115, Gln165 And Trp209 Contribute To The
1,2-Epoxy-3-(P- Nitrophenoxy)propane Conjugating
Activities Of Glutathione S-Transferase Cgstm1-1
pdb|1C72|C Chain C, Tyr115, Gln165 And Trp209 Contribute To The
1,2-Epoxy-3-(P- Nitrophenoxy)propane Conjugating
Activities Of Glutathione S-Transferase Cgstm1-1
pdb|1C72|D Chain D, Tyr115, Gln165 And Trp209 Contribute To The
1,2-Epoxy-3-(P- Nitrophenoxy)propane Conjugating
Activities Of Glutathione S-Transferase Cgstm1-1
Length = 219
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 8/62 (12%)
Query: 710 EIDKNLIKLLENGSEVVQHHAIVTLKAFYELAGSPANASLRPANLNLLPWQVRLRLERFI 769
E++K + +LEN H + AF L SP L+PA L LLP ++R +L RF+
Sbjct: 90 EVEKQRVDVLEN-------HLMDLRMAFARLCYSPDFEKLKPAYLELLPGKLR-QLSRFL 141
Query: 770 IS 771
S
Sbjct: 142 GS 143
>pdb|1G4A|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4A|F Chain F, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|F Chain F, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|K Chain K, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1G4B|L Chain L, Crystal Structures Of The Hslvu Peptidase-Atpase Complex
Reveal An Atp-Dependent Proteolysis Mechanism
pdb|1YYF|A Chain A, Correction Of X-Ray Intensities From An Hslv-Hslu Co-
Crystal Containing Lattice Translocation Defects
pdb|1YYF|B Chain B, Correction Of X-Ray Intensities From An Hslv-Hslu Co-
Crystal Containing Lattice Translocation Defects
Length = 443
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 42/69 (60%), Gaps = 10/69 (14%)
Query: 143 ELTAQEVPTRL------KVKAEQGYPISSKSKFLRKLLEQEETHQV----ILIVGLSGIG 192
E+T +E+ + L + A++ I+ ++++ R L +E H+V IL++G +G+G
Sbjct: 3 EMTPREIVSELDKHIIGQDNAKRSVAIALRNRWRRMQLNEELRHEVTPKNILMIGPTGVG 62
Query: 193 KSCLARQVA 201
K+ +AR++A
Sbjct: 63 KTEIARRLA 71
>pdb|1DO2|A Chain A, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|B Chain B, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|C Chain C, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO2|D Chain D, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From
Escherichia Coli
pdb|1DO0|A Chain A, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|B Chain B, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|C Chain C, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|D Chain D, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|E Chain E, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
pdb|1DO0|F Chain F, Orthorhombic Crystal Form Of Heat Shock Locus U (Hslu)
From Escherichia Coli
Length = 442
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 42/69 (60%), Gaps = 10/69 (14%)
Query: 143 ELTAQEVPTRL------KVKAEQGYPISSKSKFLRKLLEQEETHQV----ILIVGLSGIG 192
E+T +E+ + L + A++ I+ ++++ R L +E H+V IL++G +G+G
Sbjct: 2 EMTPREIVSELDKHIIGQDNAKRSVAIALRNRWRRMQLNEELRHEVTPKNILMIGPTGVG 61
Query: 193 KSCLARQVA 201
K+ +AR++A
Sbjct: 62 KTEIARRLA 70
>pdb|1E94|E Chain E, Hslv-Hslu From E.Coli
pdb|1E94|F Chain F, Hslv-Hslu From E.Coli
pdb|1HT2|E Chain E, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|F Chain F, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|G Chain G, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT2|H Chain H, Nucleotide-dependent Conformational Changes In A
Protease-associated Atpase Hslu
pdb|1HT1|E Chain E, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|F Chain F, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|G Chain G, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HT1|I Chain I, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HQY|E Chain E, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
pdb|1HQY|F Chain F, Nucleotide-Dependent Conformational Changes In A
Protease-Associated Atpase Hslu
Length = 449
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 42/69 (60%), Gaps = 10/69 (14%)
Query: 143 ELTAQEVPTRL------KVKAEQGYPISSKSKFLRKLLEQEETHQV----ILIVGLSGIG 192
E+T +E+ + L + A++ I+ ++++ R L +E H+V IL++G +G+G
Sbjct: 9 EMTPREIVSELDKHIIGQDNAKRSVAIALRNRWRRMQLNEELRHEVTPKNILMIGPTGVG 68
Query: 193 KSCLARQVA 201
K+ +AR++A
Sbjct: 69 KTEIARRLA 77
>pdb|1G3I|A Chain A, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|B Chain B, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|C Chain C, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|D Chain D, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|E Chain E, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|F Chain F, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|S Chain S, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|T Chain T, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|U Chain U, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|V Chain V, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|W Chain W, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G3I|X Chain X, Crystal Structure Of The Hsluv Protease-Chaperone Complex
pdb|1G41|A Chain A, Crystal Structure Of Hslu Haemophilus Influenzae
pdb|1KYI|A Chain A, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|B Chain B, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|C Chain C, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|D Chain D, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|E Chain E, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|F Chain F, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|S Chain S, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|T Chain T, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|U Chain U, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|V Chain V, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|W Chain W, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
pdb|1KYI|X Chain X, Hsluv (h. Influenzae)-nlvs Vinyl Sulfone Inhibitor Complex
Length = 444
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 42/69 (60%), Gaps = 10/69 (14%)
Query: 143 ELTAQEVPTRL------KVKAEQGYPISSKSKFLRKLLEQEETHQV----ILIVGLSGIG 192
E+T +E+ + L + A++ I+ ++++ R L++ H+V IL++G +G+G
Sbjct: 3 EMTPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVG 62
Query: 193 KSCLARQVA 201
K+ +AR++A
Sbjct: 63 KTEIARRLA 71
>pdb|1OFH|A Chain A, Asymmetric Complex Between Hslv And I-domain Deleted Hslu
(h. Influenzae)
pdb|1OFH|B Chain B, Asymmetric Complex Between Hslv And I-domain Deleted Hslu
(h. Influenzae)
pdb|1OFH|C Chain C, Asymmetric Complex Between Hslv And I-domain Deleted Hslu
(h. Influenzae)
pdb|1OFI|A Chain A, Asymmetric Complex Between Hslv And I-Domain Deleted Hslu
(H. Influenzae)
pdb|1OFI|B Chain B, Asymmetric Complex Between Hslv And I-Domain Deleted Hslu
(H. Influenzae)
pdb|1OFI|C Chain C, Asymmetric Complex Between Hslv And I-Domain Deleted Hslu
(H. Influenzae)
Length = 310
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 42/69 (60%), Gaps = 10/69 (14%)
Query: 143 ELTAQEVPTRL------KVKAEQGYPISSKSKFLRKLLEQEETHQV----ILIVGLSGIG 192
E+T +E+ + L + A++ I+ ++++ R L++ H+V IL++G +G+G
Sbjct: 3 EMTPREIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVG 62
Query: 193 KSCLARQVA 201
K+ +AR++A
Sbjct: 63 KTEIARRLA 71
>pdb|1VOK|A Chain A, Arabidopsis Thaliana Tbp (Dimer)
pdb|1VOK|B Chain B, Arabidopsis Thaliana Tbp (Dimer)
pdb|1VOL|B Chain B, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
Ternary Complex
pdb|1QN5|A Chain A, Crystal Structure Of The G(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN5|B Chain B, Crystal Structure Of The G(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN6|A Chain A, Crystal Structure Of The T(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN6|B Chain B, Crystal Structure Of The T(-26) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN7|A Chain A, Crystal Structure Of The T(-27) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN7|B Chain B, Crystal Structure Of The T(-27) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN8|A Chain A, Crystal Structure Of The T(-28) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN8|B Chain B, Crystal Structure Of The T(-28) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN9|A Chain A, Crystal Structure Of The C(-29) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN9|B Chain B, Crystal Structure Of The C(-29) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNA|A Chain A, Crystal Structure Of The T(-30) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNA|B Chain B, Crystal Structure Of The T(-30) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNB|A Chain A, Crystal Structure Of The T(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNB|B Chain B, Crystal Structure Of The T(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNC|A Chain A, Crystal Structure Of The A(-31) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNC|B Chain B, Crystal Structure Of The A(-31) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QNE|A Chain A, Crystal Structure Of The Adenovirus Major Late Promoter
Tata Box Bound To Wild-Type Tbp (Arabidopsis Thaliana
Tbp Isoform 2).
pdb|1QNE|B Chain B, Crystal Structure Of The Adenovirus Major Late Promoter
Tata Box Bound To Wild-Type Tbp (Arabidopsis Thaliana
Tbp Isoform 2).
pdb|1QN3|A Chain A, Crystal Structure Of The C(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN3|B Chain B, Crystal Structure Of The C(-25) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN4|A Chain A, Crystal Structure Of The T(-24) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution.
pdb|1QN4|B Chain B, Crystal Structure Of The T(-24) Adenovirus Major Late
Promoter Tata Box Variant Bound To Wild-Type Tbp
(Arabidopsis Thaliana Tbp Isoform 2). Tata Element
Recognition By The Tata Box-Binding Protein Has Been
Conserved Throughout Evolution
Length = 200
Score = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 222 SRAACNGSKS-DYQKRLARKISKFLVQIGFWKKIKD 256
+ C G+KS D+ K ARK ++ + ++GF K KD
Sbjct: 77 GKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKD 112
>pdb|1VTO|A Chain A, 1.9 A Resolution Refined Structure Of Tbp Recognizing The
Minor Groove Of Tataaaag
pdb|1VTO|B Chain B, 1.9 A Resolution Refined Structure Of Tbp Recognizing The
Minor Groove Of Tataaaag
Length = 190
Score = 30.8 bits (68), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 222 SRAACNGSKS-DYQKRLARKISKFLVQIGFWKKIKD 256
+ C G+KS D+ K ARK ++ + ++GF K KD
Sbjct: 67 GKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKD 102
>pdb|1VTL|E Chain E, Co-Crystal Structure Of Tbp Recognizing The Minor Groove
Of A Tata Element
pdb|1VTL|F Chain F, Co-Crystal Structure Of Tbp Recognizing The Minor Groove
Of A Tata Element
Length = 186
Score = 30.8 bits (68), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 222 SRAACNGSKS-DYQKRLARKISKFLVQIGFWKKIKD 256
+ C G+KS D+ K ARK ++ + ++GF K KD
Sbjct: 65 GKMVCTGAKSEDFSKMAARKYARIVQKLGFPAKFKD 100
>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 = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 152 RLKVKAEQGYPISSKSKFLRKLLEQEETHQVILIVGLSGIGKSCLARQVA 201
RL+++A + + +++F+ LE H+++LI G + GKS RQ A
Sbjct: 550 RLQIRAGRHPVVERRTEFVPNDLEX--AHELVLITGPNXAGKSTFLRQTA 597
>pdb|1GSU|A Chain A, An Avian Class-Mu Glutathione S-Transferase, Cgstm1-1 At
1.94 Angstrom Resolution
pdb|1GSU|B Chain B, An Avian Class-Mu Glutathione S-Transferase, Cgstm1-1 At
1.94 Angstrom Resolution
Length = 219
Score = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 710 EIDKNLIKLLENGSEVVQHHAIVTLKAFYELAGSPANASLRPANLNLLPWQVRLRLERFI 769
E++K + +LEN H + AF L SP L+PA L LP ++R +L RF+
Sbjct: 90 EVEKQRVDVLEN-------HLMDLRMAFARLCYSPDFEKLKPAYLEQLPGKLR-QLSRFL 141
Query: 770 IS 771
S
Sbjct: 142 GS 143
>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts
pdb|1EWR|B Chain B, Crystal Structure Of Taq Muts
Length = 649
Score = 30.0 bits (66), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 152 RLKVKAEQGYPISSKSKFLRKLLEQEETHQVILIVGLSGIGKSCLARQVA 201
RL+++A + + +++F+ LE H+++LI G + GKS RQ A
Sbjct: 434 RLQIRAGRHPVVERRTEFVPNDLEX--AHELVLITGPNXAGKSTFLRQTA 481
>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 = 30.0 bits (66), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 152 RLKVKAEQGYPISSKSKFLRKLLEQEETHQVILIVGLSGIGKSCLARQVA 201
RL+++A + + +++F+ LE H+++LI G + GKS RQ A
Sbjct: 550 RLQIRAGRHPVVERRTEFVPNDLEX--AHELVLITGPNXAGKSTFLRQTA 597
>pdb|3V30|A Chain A, Crystal Structure Of The Peptide Bound Complex Of The
Ankyrin Repeat Domains Of Human Rfxank
Length = 172
Score = 30.0 bits (66), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 70 HQLKSLNSLIERLHPKIRKARRMVSKSKIKNLAHVVWTSMAGDPLRKLLNSINDDLNWWL 129
HQL + L ++L +RK +V+K + ++W S G+ + ++ L W
Sbjct: 7 HQLAAQGEL-DQLKEHLRKGDNLVNKPDERGFTPLIWASAFGE-----IETVRFLLEWGA 60
Query: 130 ESQILAQNVEKVIELTA 146
+ ILA+ E + L +
Sbjct: 61 DPHILAKERESALSLAS 77
>pdb|3UXG|A Chain A, Crystal Structure Of Rfxank
Length = 172
Score = 30.0 bits (66), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 70 HQLKSLNSLIERLHPKIRKARRMVSKSKIKNLAHVVWTSMAGDPLRKLLNSINDDLNWWL 129
HQL + L ++L +RK +V+K + ++W S G+ + ++ L W
Sbjct: 7 HQLAAQGEL-DQLKEHLRKGDNLVNKPDERGFTPLIWASAFGE-----IETVRFLLEWGA 60
Query: 130 ESQILAQNVEKVIELTA 146
+ ILA+ E + L +
Sbjct: 61 DPHILAKERESALSLAS 77
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 29.6 bits (65), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 35 PKRIR-SLEDFVCDLENLMRRIKQKHAYKLHNPQLDHQLKSLNSLIERLHPKIRKARR 91
P+++R SLED + L+NL RI+Q A+ + LK N++I LH + K R
Sbjct: 61 PRKVRKSLEDTLQKLKNLPNRIRQYSAFDHAQNLIKIYLKG-NAIITDLHSEAIKDRH 117
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein
Motor Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein
Motor Domain
Length = 3245
Score = 29.6 bits (65), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 35 PKRIR-SLEDFVCDLENLMRRIKQKHAYKLHNPQLDHQLKSLNSLIERLHPKIRKARR 91
P+++R SLED + L+NL RI+Q A+ + LK N++I LH + K R
Sbjct: 61 PRKVRKSLEDTLQKLKNLPNRIRQYSAFDHAQNLIKIYLKG-NAIITDLHSEAIKDRH 117
>pdb|1IM2|A Chain A, Hslu, Haemophilus Influenzae, Selenomethionine Variant
Length = 444
Score = 29.3 bits (64), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 10/69 (14%)
Query: 143 ELTAQEVPTRL------KVKAEQGYPISSKSKFLRKLLEQEETHQV----ILIVGLSGIG 192
E T +E+ + L + A++ I+ ++++ R L++ H+V IL +G +G+G
Sbjct: 3 EXTPREIVSELDQHIIGQADAKRAVAIALRNRWRRXQLQEPLRHEVTPKNILXIGPTGVG 62
Query: 193 KSCLARQVA 201
K+ +AR++A
Sbjct: 63 KTEIARRLA 71
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 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,793,297
Number of Sequences: 62578
Number of extensions: 870437
Number of successful extensions: 2565
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 34
Number of HSP's that attempted gapping in prelim test: 2557
Number of HSP's gapped (non-prelim): 42
length of query: 862
length of database: 14,973,337
effective HSP length: 107
effective length of query: 755
effective length of database: 8,277,491
effective search space: 6249505705
effective search space used: 6249505705
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: 56 (26.2 bits)