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= 013323
(445 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3GLH|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|C Chain C, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|D Chain D, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|G Chain G, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|H Chain H, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|I Chain I, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|L Chain L, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|M Chain M, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|N Chain N, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
Length = 376
Score = 31.6 bits (70), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 82 LIVGTMKGSRLQDTFFFRDQMKANGFLPDVAVYNYLISVCGKCKNSDQAIRIFEEMKKYE 141
L+ +GS L+D DQ A+G D V +S + DQA+ + E M
Sbjct: 208 LLARAAEGS-LRDALSLTDQAIASG---DGQVSTQAVSAMLGTLDDDQALSLVEAM---- 259
Query: 142 VKPNGQTYVCLLNACAAAG 160
V+ NG+ + L+N AA G
Sbjct: 260 VEANGERVMALINEAAARG 278
>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|B Chain B, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|C Chain C, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1XXH|B Chain B, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|C Chain C, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|D Chain D, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|G Chain G, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|H Chain H, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|I Chain I, Atpgs Bound E. Coli Clamp Loader Complex
Length = 373
Score = 31.6 bits (70), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 82 LIVGTMKGSRLQDTFFFRDQMKANGFLPDVAVYNYLISVCGKCKNSDQAIRIFEEMKKYE 141
L+ +GS L+D DQ A+G D V +S + DQA+ + E M
Sbjct: 205 LLARAAEGS-LRDALSLTDQAIASG---DGQVSTQAVSAMLGTLDDDQALSLVEAM---- 256
Query: 142 VKPNGQTYVCLLNACAAAG 160
V+ NG+ + L+N AA G
Sbjct: 257 VEANGERVMALINEAAARG 275
>pdb|1ZE1|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|B Chain B, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|C Chain C, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE1|D Chain D, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
Length = 309
Score = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 55/127 (43%), Gaps = 10/127 (7%)
Query: 321 SEKFPPAELYATLVEGAMFGYTPKGMQLAQDTLVNMNSRNIF----LSPRMGSDLLLVAA 376
++K+ LY EG + PK +++ + VN+ R++ +SP L +
Sbjct: 119 AKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDI 178
Query: 377 GEKSG-GYTTANYIWDLMQARKITPSLPAVEAYYNGLKDREVPADD-----PRLVVVSRA 430
G K G G T + + + I SL EA +++R +P + PR+VV +
Sbjct: 179 GYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQES 238
Query: 431 YDNLLRG 437
+L G
Sbjct: 239 TKMILNG 245
>pdb|1ZE2|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
pdb|1ZE2|B Chain B, Conformational Change Of Pseudouridine 55 Synthase Upon
Its Association With Rna Substrate
Length = 309
Score = 31.6 bits (70), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 55/127 (43%), Gaps = 10/127 (7%)
Query: 321 SEKFPPAELYATLVEGAMFGYTPKGMQLAQDTLVNMNSRNIF----LSPRMGSDLLLVAA 376
++K+ LY EG + PK +++ + VN+ R++ +SP L +
Sbjct: 119 AKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDI 178
Query: 377 GEKSG-GYTTANYIWDLMQARKITPSLPAVEAYYNGLKDREVPADD-----PRLVVVSRA 430
G K G G T + + + I SL EA +++R +P + PR+VV +
Sbjct: 179 GYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQES 238
Query: 431 YDNLLRG 437
+L G
Sbjct: 239 TKMILNG 245
>pdb|2AB4|A Chain A, Dissecting The Roles Of A Strictly Conserved Tyrosine In
Substrate Recognition And Catalysis By Pseudouridine 55
Synthase
Length = 309
Score = 31.6 bits (70), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 55/127 (43%), Gaps = 10/127 (7%)
Query: 321 SEKFPPAELYATLVEGAMFGYTPKGMQLAQDTLVNMNSRNIF----LSPRMGSDLLLVAA 376
++K+ LY EG + PK +++ + VN+ R++ +SP L +
Sbjct: 119 AKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDI 178
Query: 377 GEKSG-GYTTANYIWDLMQARKITPSLPAVEAYYNGLKDREVPADD-----PRLVVVSRA 430
G K G G T + + + I SL EA +++R +P + PR+VV +
Sbjct: 179 GYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQES 238
Query: 431 YDNLLRG 437
+L G
Sbjct: 239 TKMILNG 245
>pdb|1R3E|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And
Its Rna Complex: Rna-Protein Recognition Through A
Combination Of Rigid Docking And Induced Fit
Length = 309
Score = 31.6 bits (70), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 55/127 (43%), Gaps = 10/127 (7%)
Query: 321 SEKFPPAELYATLVEGAMFGYTPKGMQLAQDTLVNMNSRNIF----LSPRMGSDLLLVAA 376
++K+ LY EG + PK +++ + VN+ R++ +SP L +
Sbjct: 119 AKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDI 178
Query: 377 GEKSG-GYTTANYIWDLMQARKITPSLPAVEAYYNGLKDREVPADD-----PRLVVVSRA 430
G K G G T + + + I SL EA +++R +P + PR+VV +
Sbjct: 179 GYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQES 238
Query: 431 YDNLLRG 437
+L G
Sbjct: 239 TKMILNG 245
>pdb|3GLG|B Chain B, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|C Chain C, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|D Chain D, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|G Chain G, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|H Chain H, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|I Chain I, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
Length = 395
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 82 LIVGTMKGSRLQDTFFFRDQMKANGFLPDVAVYNYLISVCGKCKNSDQAIRIFEEMKKYE 141
L+ +GS L+D DQ A+G D V +S + DQA+ + E M
Sbjct: 227 LLARAAEGS-LRDALSLTDQAIASG---DGQVSTQAVSAMLGTLDDDQALSLVEAM---- 278
Query: 142 VKPNGQTYVCLLNACAAAG 160
V+ NG+ + L+N AA G
Sbjct: 279 VEANGERVMALINEAAARG 297
>pdb|3GLF|B Chain B, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|C Chain C, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|D Chain D, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|G Chain G, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|H Chain H, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|I Chain I, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLI|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|C Chain C, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|D Chain D, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|G Chain G, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|H Chain H, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|I Chain I, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
Length = 395
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 82 LIVGTMKGSRLQDTFFFRDQMKANGFLPDVAVYNYLISVCGKCKNSDQAIRIFEEMKKYE 141
L+ +GS L+D DQ A+G D V +S + DQA+ + E M
Sbjct: 227 LLARAAEGS-LRDALSLTDQAIASG---DGQVSTQAVSAMLGTLDDDQALSLVEAM---- 278
Query: 142 VKPNGQTYVCLLNACAAAG 160
V+ NG+ + L+N AA G
Sbjct: 279 VEANGERVMALINEAAARG 297
>pdb|1XXI|B Chain B, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|C Chain C, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|D Chain D, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|G Chain G, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|H Chain H, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|I Chain I, Adp Bound E. Coli Clamp Loader Complex
Length = 368
Score = 31.6 bits (70), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 82 LIVGTMKGSRLQDTFFFRDQMKANGFLPDVAVYNYLISVCGKCKNSDQAIRIFEEMKKYE 141
L+ +GS L+D DQ A+G D V +S + DQA+ + E M
Sbjct: 205 LLARAAEGS-LRDALSLTDQAIASG---DGQVSTQAVSAMLGTLDDDQALSLVEAM---- 256
Query: 142 VKPNGQTYVCLLNACAAAG 160
V+ NG+ + L+N AA G
Sbjct: 257 VEANGERVMALINEAAARG 275
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
0.320 0.135 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,223,832
Number of Sequences: 62578
Number of extensions: 553081
Number of successful extensions: 1264
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1261
Number of HSP's gapped (non-prelim): 15
length of query: 445
length of database: 14,973,337
effective HSP length: 102
effective length of query: 343
effective length of database: 8,590,381
effective search space: 2946500683
effective search space used: 2946500683
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: 53 (25.0 bits)