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= 017510
(370 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LW4|A Chain A, Solution Nmr Structure Of Human Transcription Elongation
Factor A Protein 2, Central Domain, Northeast Structural
Genomics Consortium (Nesg) Target Hr8682b
Length = 113
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 36/101 (35%), Positives = 50/101 (49%), Gaps = 7/101 (6%)
Query: 190 DYFRERIREKLYKALSKVSGEVDEEVQDKLNGCDPIRVAITAESLMFEKWGHSFGTYEVK 249
D R + RE L AL V G D R++ E +F G++ Y+ +
Sbjct: 10 DAVRNKCREMLTAALQTDHDHV-------AIGADCERLSAQIEECIFRDVGNTDMKYKNR 62
Query: 250 YRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVSD 290
RS + NL D +NPD RR VL G + P+ + M+SEEM SD
Sbjct: 63 VRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASD 103
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
Finger Protein 3
Length = 120
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 36/97 (37%), Positives = 53/97 (54%), Gaps = 8/97 (8%)
Query: 193 RERIREKLYKALSKVSGEVDEEVQDKLNGCDPIRVAITAESLMFEKWGHSFGTYEVKYRS 252
R +++ L K L+ + +V EE K VA E +F + + Y+ KYRS
Sbjct: 17 RHSLKDILMKRLTDSNLKVPEEKAAK--------VATKIEKELFSFFRDTDAKYKNKYRS 68
Query: 253 ILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVS 289
++FNL DP+N +KVL G V P+ LI+MS EE+ S
Sbjct: 69 LMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELAS 105
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 41/70 (58%)
Query: 221 GCDPIRVAITAESLMFEKWGHSFGTYEVKYRSILFNLMDPENPDFRRKVLLGHVKPEALI 280
G D + E ++++ ++ Y+ + RS + NL D +NP+ R+ VL G++ P+
Sbjct: 38 GADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFA 97
Query: 281 KMSSEEMVSD 290
+M++EEM SD
Sbjct: 98 RMTAEEMASD 107
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 37/155 (23%), Positives = 64/155 (41%), Gaps = 32/155 (20%)
Query: 192 FRERIREKLYKALSKVS----------GEVDEEVQDKLNGCDPIRVAITAESLMFEKWGH 241
R+++ + LY L+K S + E +K+N CD A
Sbjct: 148 LRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAA------------- 194
Query: 242 SFGTYEVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVSDGSRRLNQQIKK 301
Y+ +YR I N++ NPD + K+ G + PE L ++++ L Q+I +
Sbjct: 195 ----YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDL---APAPLKQKI-E 246
Query: 302 ERASDRYLPWKGGYLGPIYHSTRYMCGRCGHKKTT 336
E A +G + + R+ CG+C KK +
Sbjct: 247 EIAKQNLYNAQGATIERSV-TDRFTCGKCKEKKVS 280
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/182 (23%), Positives = 73/182 (40%), Gaps = 36/182 (19%)
Query: 192 FRERIREKLYKALSKVS----------GEVDEEVQDKLNGCDPIRVAITAESLMFEKWGH 241
R+++ + LY L+K S + E +K+N CD A
Sbjct: 17 LRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAA------------- 63
Query: 242 SFGTYEVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVSDGSRRLNQQIKK 301
Y+ +YR I N++ NPD + K+ G + PE L ++++ L Q+I +
Sbjct: 64 ----YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDL---APAPLKQKI-E 115
Query: 302 ERASDRYLPWKGGYLGPIYHSTRYMCGRCGHKKTTNHGNDQNSSAKRI----KCLNCYQY 357
E A +G + + R+ CG+C KK + + S+A + C C
Sbjct: 116 EIAKQNLYNAQGATIERSV-TDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNR 174
Query: 358 WE 359
W+
Sbjct: 175 WK 176
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 35/155 (22%), Positives = 63/155 (40%), Gaps = 32/155 (20%)
Query: 192 FRERIREKLYKALSKVS----------GEVDEEVQDKLNGCDPIRVAITAESLMFEKWGH 241
R+++ + LY L+K S + E +K+N CD A
Sbjct: 12 LRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAA------------- 58
Query: 242 SFGTYEVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVSDGSRRLNQQIKK 301
Y+ +YR I N++ NPD + K+ G + PE L ++++ ++ ++I K
Sbjct: 59 ----YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAK 114
Query: 302 ERASDRYLPWKGGYLGPIYHSTRYMCGRCGHKKTT 336
+ L G + R+ CG+C KK +
Sbjct: 115 QN-----LYNAQGATIERSVTDRFTCGKCKEKKVS 144
>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|S Chain S, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
Length = 179
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 37/155 (23%), Positives = 64/155 (41%), Gaps = 32/155 (20%)
Query: 192 FRERIREKLYKALSKVS----------GEVDEEVQDKLNGCDPIRVAITAESLMFEKWGH 241
R+++ + LY L+K S + E +K+N CD A
Sbjct: 18 LRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAA------------- 64
Query: 242 SFGTYEVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVSDGSRRLNQQIKK 301
Y+ +YR I N++ NPD + K+ G + PE L ++++ L Q+I +
Sbjct: 65 ----YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDL---APAPLKQKI-E 116
Query: 302 ERASDRYLPWKGGYLGPIYHSTRYMCGRCGHKKTT 336
E A +G + + R+ CG+C KK +
Sbjct: 117 EIAKQNLYNAQGATIERSV-TDRFTCGKCKEKKVS 150
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
Length = 114
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 25/106 (23%), Positives = 44/106 (41%), Gaps = 27/106 (25%)
Query: 192 FRERIREKLYKALSKVS----------GEVDEEVQDKLNGCDPIRVAITAESLMFEKWGH 241
R+++ + LY L+K S + E +K+N CD A
Sbjct: 22 LRDQVLKALYDVLAKESEHPPQSILHTAKAIESEMNKVNNCDTNEAA------------- 68
Query: 242 SFGTYEVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEM 287
Y+ +YR I N++ NPD + K+ G + PE L ++++
Sbjct: 69 ----YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDL 110
>pdb|3NFH|A Chain A, Crystal Structure Of Tandem Winged Helix Domain Of Rna
Polymerase I Subunit A49 (P4)
pdb|3NFH|B Chain B, Crystal Structure Of Tandem Winged Helix Domain Of Rna
Polymerase I Subunit A49 (P4)
Length = 246
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 127 VEVVKVRRVDQKGAPRSKKLVGSEFIVTEETNSLDNVDAEAIREEKPASAVVPQKLVSMI 186
+++V R K P +L E + L N+DA + + P +++P+K + I
Sbjct: 6 IDIVDSVRTASKDLPTRAQL--DEITSNDRPTPLANIDATDVEQIYPIESIIPKKELQFI 63
Query: 187 KCNDYFRERIREK 199
+ + +E +EK
Sbjct: 64 RVSSILKEADKEK 76
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 0.132 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,024,739
Number of Sequences: 62578
Number of extensions: 382377
Number of successful extensions: 894
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 879
Number of HSP's gapped (non-prelim): 14
length of query: 370
length of database: 14,973,337
effective HSP length: 100
effective length of query: 270
effective length of database: 8,715,537
effective search space: 2353194990
effective search space used: 2353194990
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)