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= 037763
(354 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
Finger Protein 3
Length = 120
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 36/109 (33%), Positives = 59/109 (54%), Gaps = 7/109 (6%)
Query: 176 DCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTY 235
D IR+ VR L L K ++ N ++ ++ A +VA +E ++ + + Y
Sbjct: 10 DQIRQSVRHSLKDILMKRLTDS---NLKVPEEKAA----KVATKIEKELFSFFRDTDAKY 62
Query: 236 KFKYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQLW 284
K KYR L+FN+ DP N KKVL G V P+ ++ M+ +E+AS ++ W
Sbjct: 63 KNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAW 111
>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 = 55.5 bits (132), Expect = 5e-08, Method: Composition-based stats.
Identities = 33/107 (30%), Positives = 56/107 (52%), Gaps = 10/107 (9%)
Query: 176 DCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTY 235
D +R RE L AL + HD+ I D +++ +E I+ + G + Y
Sbjct: 10 DAVRNKCREMLTAAL-----QTDHDHVAI-----GADCERLSAQIEECIFRDVGNTDMKY 59
Query: 236 KFKYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQ 282
K + R + N+ D N + R+ VL G + P++I MT++EMASD+++
Sbjct: 60 KNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELK 106
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 51.2 bits (121), Expect = 9e-07, Method: Composition-based stats.
Identities = 36/115 (31%), Positives = 51/115 (44%), Gaps = 10/115 (8%)
Query: 166 PNASNSLKCNDCIREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIY 225
P + +D +R RE L AL G D I D ++ +E AIY
Sbjct: 4 PFTPRAPSTSDSVRLKCREMLAAAL-----RTGDDYIAI-----GADEEELGSQIEEAIY 53
Query: 226 ENWGRSTGTYKFKYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDK 280
+ + YK + R + N+ D N RK VL G + P+ MTA+EMASD+
Sbjct: 54 QEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDE 108
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 40/174 (22%), Positives = 70/174 (40%), Gaps = 24/174 (13%)
Query: 178 IREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKF 237
+R+ V + LY L+K SE H + I+ +A I E N + YK
Sbjct: 12 LRDQVLKALYDVLAKESE---HPPQSILHTAKA-------IESEMNKVNNCDTNEAAYKA 61
Query: 238 KYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQLWYENLEKERAGTNG 297
+YR + N+ N + + K+ G + PE + AK++A ++ E + K+ N
Sbjct: 62 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQ----NL 117
Query: 298 RIFSGIVSPKKIISGICKCGRCRHTRMSFISLRRHIA---------CLNCNQYW 342
G + + CG+C+ ++S+ L+ A C C W
Sbjct: 118 YNAQGATIERSVTDRF-TCGKCKEKKVSYYQLQTRSADHPLTTFCTCEACGNRW 170
>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 = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 40/174 (22%), Positives = 70/174 (40%), Gaps = 24/174 (13%)
Query: 178 IREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKF 237
+R+ V + LY L+K SE H + I+ +A I E N + YK
Sbjct: 18 LRDQVLKALYDVLAKESE---HPPQSILHTAKA-------IESEMNKVNNCDTNEAAYKA 67
Query: 238 KYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQLWYENLEKERAGTNG 297
+YR + N+ N + + K+ G + PE + AK++A ++ E + K+ N
Sbjct: 68 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQ----NL 123
Query: 298 RIFSGIVSPKKIISGICKCGRCRHTRMSFISLRRHIA---------CLNCNQYW 342
G + + CG+C+ ++S+ L+ A C C W
Sbjct: 124 YNAQGATIERSVTDRFT-CGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRW 176
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 40/174 (22%), Positives = 70/174 (40%), Gaps = 24/174 (13%)
Query: 178 IREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKF 237
+R+ V + LY L+K SE H + I+ +A I E N + YK
Sbjct: 17 LRDQVLKALYDVLAKESE---HPPQSILHTAKA-------IESEMNKVNNCDTNEAAYKA 66
Query: 238 KYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQLWYENLEKERAGTNG 297
+YR + N+ N + + K+ G + PE + AK++A ++ E + K+ N
Sbjct: 67 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQ----NL 122
Query: 298 RIFSGIVSPKKIISGICKCGRCRHTRMSFISLRRHIA---------CLNCNQYW 342
G + + CG+C+ ++S+ L+ A C C W
Sbjct: 123 YNAQGATIERSVTDRF-TCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRW 175
>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 = 40/174 (22%), Positives = 70/174 (40%), Gaps = 24/174 (13%)
Query: 178 IREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKF 237
+R+ V + LY L+K SE H + I+ +A I E N + YK
Sbjct: 148 LRDQVLKALYDVLAKESE---HPPQSILHTAKA-------IESEMNKVNNCDTNEAAYKA 197
Query: 238 KYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMASDKMQLWYENLEKERAGTNG 297
+YR + N+ N + + K+ G + PE + AK++A ++ E + K+ N
Sbjct: 198 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQ----NL 253
Query: 298 RIFSGIVSPKKIISGICKCGRCRHTRMSFISLRRHIA---------CLNCNQYW 342
G + + CG+C+ ++S+ L+ A C C W
Sbjct: 254 YNAQGATIERSVTDRFT-CGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRW 306
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
Length = 114
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 10/100 (10%)
Query: 178 IREIVREKLYGALSKVSEEAGHDNKEIIDQVRACDPIQVAISVESAIYENWGRSTGTYKF 237
+R+ V + LY L+K SE H + I+ +A I E N + YK
Sbjct: 22 LRDQVLKALYDVLAKESE---HPPQSILHTAKA-------IESEMNKVNNCDTNEAAYKA 71
Query: 238 KYRCLLFNINDPTNREFRKKVLLGRVKPEKIVNMTAKEMA 277
+YR + N+ N + + K+ G + PE + AK++A
Sbjct: 72 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111
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 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,831,396
Number of Sequences: 62578
Number of extensions: 368984
Number of successful extensions: 737
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 724
Number of HSP's gapped (non-prelim): 9
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
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: 52 (24.6 bits)