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= 026167
(242 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1F3U|A Chain A, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
Human Tfiif
pdb|1F3U|C Chain C, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
Human Tfiif
pdb|1F3U|E Chain E, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
Human Tfiif
pdb|1F3U|G Chain G, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
Human Tfiif
Length = 118
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 32/118 (27%), Positives = 60/118 (50%), Gaps = 12/118 (10%)
Query: 11 GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTM-E 69
G+ +L AK + VWL+K P +++ W A + V K+ ++ +++ + FT+ E
Sbjct: 4 GELDLTGAKQNTGVWLVKVPKYLSQQW---AKASGRGEVGKLRIAKTQGRTE-VSFTLNE 59
Query: 70 TTAVSNDSLNRPKSYSLNMFKDFV-------PMSVFSESNQGKVAMEGKVEHKFDMKP 120
A +D +P S S FV ++VF+ES+ K+++EG V + + +P
Sbjct: 60 DLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRP 117
>pdb|1BBY|A Chain A, Dna-Binding Domain From Human Rap30, Nmr, Minimized
Average
pdb|2BBY|A Chain A, Dna-Binding Domain From Human Rap30, Nmr, 30 Structures
Length = 69
Score = 30.8 bits (68), Expect = 0.71, Method: Composition-based stats.
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 189 RRDRGELEDIMFKLFERQPNWALKQLVQETDQPAVWF 225
R D+ + D++F FE+ + LK LV T QP V+
Sbjct: 3 RADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYL 39
>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With
An 8-Base Single-Stranded Dna Oligonucleotide
Length = 659
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 25/55 (45%)
Query: 132 CRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVK 186
CR + + Q+ID +R G+V S S DKKKA P K++ K
Sbjct: 586 CRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKK 640
>pdb|2O19|A Chain A, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O19|B Chain B, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O54|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O54|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O59|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O59|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O5C|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5C|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5E|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
pdb|2O5E|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
Length = 659
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 25/55 (45%)
Query: 132 CRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVK 186
CR + + Q+ID +R G+V S S DKKKA P K++ K
Sbjct: 586 CRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKK 640
>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii
Length = 653
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 25/55 (45%)
Query: 132 CRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVK 186
CR + + Q+ID +R G+V S S DKKKA P K++ K
Sbjct: 586 CRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKK 640
>pdb|1YA9|A Chain A, Crystal Structure Of The 22kda N-Terminal Fragment Of
Mouse Apolipoprotein E
Length = 181
Score = 27.7 bits (60), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 29/66 (43%)
Query: 63 SMQFTMETTAVSNDSLNRPKSYSLNMFKDFVPMSVFSESNQGKVAMEGKVEHKFDMKPHE 122
S Q T E TA+ D++ K+Y + + P++ + + GK + DM+
Sbjct: 44 SSQVTQELTALMEDTMTEVKAYKKELEEQLGPVAEETRARLGKEVQAAQARLGADMEDLR 103
Query: 123 KNMEEY 128
+ +Y
Sbjct: 104 NRLGQY 109
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
0.316 0.130 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,949,966
Number of Sequences: 62578
Number of extensions: 250266
Number of successful extensions: 617
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 611
Number of HSP's gapped (non-prelim): 6
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
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: 50 (23.9 bits)