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= psy996
(221 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 83.6 bits (205), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 49/114 (42%), Positives = 63/114 (55%), Gaps = 13/114 (11%)
Query: 45 KSHNLTDSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTDNRYKNRV 104
++ + +DSVRLKCREML +++ GD + IY E +NTD +YKNRV
Sbjct: 8 RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYKNRV 67
Query: 105 RSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDE 158
RSRI+NLKD KNP L +N + G I A MTAE EMA+DE
Sbjct: 68 RSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE-------------EMASDE 108
>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 = 82.4 bits (202), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 47/113 (41%), Positives = 63/113 (55%), Gaps = 13/113 (11%)
Query: 51 DSVRLKCREMLQNSIQVGDLDMDGXXXXXXXXXXXXXXIYNEFKNTDNRYKNRVRSRIAN 110
D+VR KCREML ++Q + I+ + NTD +YKNRVRSRI+N
Sbjct: 10 DAVRNKCREMLTAALQTDHDHVAIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISN 69
Query: 111 LKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLR 163
LKD KNP L RN + GAI+ ++A MT+E EMA+DE+K +R
Sbjct: 70 LKDAKNPDLRRNVLCGAITPQQIAVMTSE-------------EMASDELKEIR 109
>pdb|1TFI|A Chain A, A Novel Zn Finger Motif In The Basal Transcriptional
Machinery: Three-Dimensional Nmr Studies Of The Nucleic-
Acid Binding Domain Of Transcriptional Elongation Factor
Tfiis
Length = 50
Score = 63.9 bits (154), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 28/34 (82%), Positives = 30/34 (88%)
Query: 181 GTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
GT+TDL CGKCKK+NCTY QVQTRSADEPMTT
Sbjct: 4 GTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTF 37
Score = 35.0 bits (79), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 20/34 (58%)
Query: 124 IFGAISASKLATMTAEVQTRSADEPMTTFEMAND 157
+F K +VQTRSADEPMTTF + N+
Sbjct: 9 LFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE 42
>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 = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 40/115 (34%), Positives = 60/115 (52%), Gaps = 13/115 (11%)
Query: 100 YKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEM 159
YK R R +N+ NP L G I+ LAT A+ ++A +
Sbjct: 65 YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAK-------------DLAPAPL 111
Query: 160 KTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
K + K+++ +AQ AT++ + TD CGKCK++ +Y Q+QTRSADEP+TT
Sbjct: 112 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTF 166
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 40/115 (34%), Positives = 60/115 (52%), Gaps = 13/115 (11%)
Query: 100 YKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEM 159
YK R R +N+ NP L G I+ LAT A+ ++A +
Sbjct: 195 YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAK-------------DLAPAPL 241
Query: 160 KTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
K + K+++ +AQ AT++ + TD CGKCK++ +Y Q+QTRSADEP+TT
Sbjct: 242 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTF 296
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 60.5 bits (145), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 39/115 (33%), Positives = 59/115 (51%), Gaps = 13/115 (11%)
Query: 100 YKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEM 159
YK R R +N+ NP L G I+ LAT A+ ++A +
Sbjct: 59 YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAK-------------DLAPAPL 105
Query: 160 KTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
K + K+++ +AQ AT++ + TD CGKCK++ +Y Q+QTRSAD P+TT
Sbjct: 106 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADHPLTTF 160
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 57.0 bits (136), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 38/115 (33%), Positives = 58/115 (50%), Gaps = 13/115 (11%)
Query: 100 YKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEM 159
YK R R +N+ NP L G I+ LAT A+ ++A +
Sbjct: 64 YKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAK-------------DLAPAPL 110
Query: 160 KTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTL 214
K + K+++ +AQ AT++ + TD CGKCK++ +Y Q+QTRSA P+TT
Sbjct: 111 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTF 165
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
Finger Protein 3
Length = 120
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 13/77 (16%)
Query: 89 IYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEP 148
+++ F++TD +YKN+ RS + NLKDPKN +L + + G ++ L M+ E
Sbjct: 51 LFSFFRDTDAKYKNKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPE--------- 101
Query: 149 MTTFEMANDEMKTLRNK 165
E+A+ E+ R +
Sbjct: 102 ----ELASKELAAWRRR 114
>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 133
Score = 34.7 bits (78), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 188 KCGKCKKRNCTYNQVQTRSADEPMTTLH 215
+C KC R + Q+Q RSADEPMTT +
Sbjct: 94 ECPKCHSRENVFFQLQIRSADEPMTTFY 121
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 139 EVQTRSADEPMTTF 152
++Q RSADEPMTTF
Sbjct: 107 QLQIRSADEPMTTF 120
>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures
Length = 57
Score = 27.7 bits (60), Expect = 5.5, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 173 DAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLH 215
+ L T+ TK + C KC + ++QTR+ DEP T +
Sbjct: 5 EQDLKTLPTTK---ITCPKCGNDTAYWWEMQTRAGDEPSTIFY 44
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
0.318 0.131 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,942,402
Number of Sequences: 62578
Number of extensions: 144882
Number of successful extensions: 436
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 412
Number of HSP's gapped (non-prelim): 17
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
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: 49 (23.5 bits)