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= 035641
(314 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 101 bits (252), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 46/114 (40%), Positives = 71/114 (62%)
Query: 200 AEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFM 259
A K ++R I N+ + NPDL+ ++ G++TPE LAT ++LA +Q+ EEI + +
Sbjct: 194 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNL 253
Query: 260 FKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
+ + ++ TD+F C C + SY+Q+QTRSADEP+TT+ TC C RWK
Sbjct: 254 YNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWK 307
>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 = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 46/114 (40%), Positives = 71/114 (62%)
Query: 200 AEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFM 259
A K ++R I N+ + NPDL+ ++ G++TPE LAT ++LA +Q+ EEI + +
Sbjct: 64 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNL 123
Query: 260 FKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
+ + ++ TD+F C C + SY+Q+QTRSADEP+TT+ TC C RWK
Sbjct: 124 YNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWK 177
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 98.6 bits (244), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 45/114 (39%), Positives = 70/114 (61%)
Query: 200 AEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFM 259
A K ++R I N+ + NPDL+ ++ G++TPE LAT ++LA +Q+ EEI + +
Sbjct: 58 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNL 117
Query: 260 FKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
+ + ++ TD+F C C + SY+Q+QTRSAD P+TT+ TC C RWK
Sbjct: 118 YNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADHPLTTFCTCEACGNRWK 171
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 95.5 bits (236), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 44/114 (38%), Positives = 69/114 (60%)
Query: 200 AEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQENEEIKAKFM 259
A K ++R I N+ + NPDL+ ++ G++TPE LAT ++LA +Q+ EEI + +
Sbjct: 63 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNL 122
Query: 260 FKCEVPEKKKGTTDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
+ + ++ TD+F C C + SY+Q+QTRSA P+TT+ TC C RWK
Sbjct: 123 YNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRWK 176
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
Finger Protein 3
Length = 120
Score = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 38/100 (38%), Positives = 57/100 (57%), Gaps = 2/100 (2%)
Query: 147 DKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHR 206
D+IR+ + +L + + D + +V +VA +E+ +F R K K+R
Sbjct: 10 DQIRQSVRHSLKDILMKRLTDSNL--KVPEEKAAKVATKIEKELFSFFRDTDAKYKNKYR 67
Query: 207 SIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDE 246
S+MFN+ D KN L ++VL GEVTP+ L M+PEELAS E
Sbjct: 68 SLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKE 107
>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 = 65.1 bits (157), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 31/48 (64%), Positives = 34/48 (70%), Gaps = 1/48 (2%)
Query: 267 KKKGT-TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
K GT TD F C C K NC+Y Q+QTRSADEPMTT+V C EC RWK
Sbjct: 1 KTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK 48
>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 = 63.9 bits (154), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 38/107 (35%), Positives = 62/107 (57%), Gaps = 9/107 (8%)
Query: 143 DSMRDKIRKDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEK 202
D++R+K R+ L AL D + + D ++++A +E +F + + K
Sbjct: 10 DAVRNKCREMLTAALQ------TDHDHVA---IGADCERLSAQIEECIFRDVGNTDMKYK 60
Query: 203 RKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDERRQ 249
+ RS + N+ D KNPDLRR VL G +TP+++A MT EE+ASDE ++
Sbjct: 61 NRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELKE 107
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 38/113 (33%), Positives = 59/113 (52%), Gaps = 15/113 (13%)
Query: 137 HADQAKDSMRDKIRKDLEKAL---SRVASEAADDEEITDRVKARDPKQVAASVERVMFEK 193
A DS+R K R+ L AL + AD+EE+ + +E ++++
Sbjct: 8 RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEEL------------GSQIEEAIYQE 55
Query: 194 LRPMGVAEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELASDE 246
+R + K + RS + N+ D KNP+LR+ VL G + P+ A MT EE+ASDE
Sbjct: 56 IRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDE 108
>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 133
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%)
Query: 276 KCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
+C C + Q+Q RSADEPMTT+ C C RWK
Sbjct: 94 ECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGHRWK 131
>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures
Length = 57
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 272 TDQFKCSGCGKSNCSYHQMQTRSADEPMTTYVTCAECNKRWK 313
T + C CG + +MQTR+ DEP T + C +C W+
Sbjct: 13 TTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWR 54
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
Length = 114
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 29/44 (65%)
Query: 200 AEKRKHRSIMFNMSDEKNPDLRRRVLIGEVTPERLATMTPEELA 243
A K ++R I N+ + NPDL+ ++ G++TPE LAT ++LA
Sbjct: 68 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111
>pdb|3IFQ|A Chain A, Interction Of Plakoglobin And Beta-Catenin With Desmosomal
Cadherins
pdb|3IFQ|B Chain B, Interction Of Plakoglobin And Beta-Catenin With Desmosomal
Cadherins
Length = 553
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 151 KDLEKALSRVASEAADDEEITDRVKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMF 210
+++++ + V E A D+E D + A AS + R G A +++F
Sbjct: 475 ENIQRVAAGVLCELAQDKEAADAIDAE-----GASAPLMELLHSRNEGTATYAA--AVLF 527
Query: 211 NMSDEKNPDLRRRV 224
+S++KNPD R+RV
Sbjct: 528 RISEDKNPDYRKRV 541
>pdb|1GPP|A Chain A, Crystal Structure Of The S.Cerevisiae Homing Endonuclease
Pi-Scei Domain I
Length = 237
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 23/46 (50%)
Query: 174 VKARDPKQVAASVERVMFEKLRPMGVAEKRKHRSIMFNMSDEKNPD 219
++ARD + + V + ++ P+G A R+ R F + + K D
Sbjct: 169 IEARDLSLLGSHVRKATYQTYAPIGAAFARECRGFYFELQELKEDD 214
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
0.313 0.126 0.357
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,168,554
Number of Sequences: 62578
Number of extensions: 300763
Number of successful extensions: 591
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 575
Number of HSP's gapped (non-prelim): 21
length of query: 314
length of database: 14,973,337
effective HSP length: 99
effective length of query: 215
effective length of database: 8,778,115
effective search space: 1887294725
effective search space used: 1887294725
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)