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= 020949
(319 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 = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 31/70 (44%), Positives = 45/70 (64%)
Query: 224 DSVRVAIALESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGM 283
D R++ +E +F G +D YK + R+ + NLKD KNPD RR VL G + P+ + M
Sbjct: 36 DCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVM 95
Query: 284 TAKEMASDEM 293
T++EMASDE+
Sbjct: 96 TSEEMASDEL 105
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
Finger Protein 3
Length = 120
Score = 65.1 bits (157), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 37/103 (35%), Positives = 62/103 (60%), Gaps = 4/103 (3%)
Query: 191 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWGRSDGPYKIK 250
D R+ VR + D L K +++ ++ +E A +VA +E +F + +D YK K
Sbjct: 10 DQIRQSVRHSLKDILMKRLTDSNLKVPEEKAA----KVATKIEKELFSFFRDTDAKYKNK 65
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASDEM 293
YR+++ NLKDPKN +KVL G+V P+ ++ M+ +E+AS E+
Sbjct: 66 YRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKEL 108
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 41/61 (67%)
Query: 232 LESAMFEKWGRSDGPYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMASD 291
+E A++++ +D YK + R+ + NLKD KNP+ R+ VL G + P+ MTA+EMASD
Sbjct: 48 IEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD 107
Query: 292 E 292
E
Sbjct: 108 E 108
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 193 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDGPYKIK 250
+ +R++V AL V + E + + A A+ES M ++ YK +
Sbjct: 13 YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 67
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
YR + N+ NPD + K+ G + PE + AK++A
Sbjct: 68 YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 106
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 193 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDGPYKIK 250
+ +R++V AL V + E + + A A+ES M ++ YK +
Sbjct: 14 YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 68
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
YR + N+ NPD + K+ G + PE + AK++A
Sbjct: 69 YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 107
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 52/224 (23%), Positives = 81/224 (36%), Gaps = 52/224 (23%)
Query: 71 IQDFASDLIVSWRDMFLEQIRD---EKKGSCTIPGDTEPAKIEKVDKRTSEECQEISGVG 127
I +I SW+D + R ++ PG+ E DK T E
Sbjct: 61 ISKLVKKMISSWKDAINKNKRSRQAQQHHQDHAPGNAE-------DKTTVGES------- 106
Query: 128 IVKVQKVDQXXXXXXXXXXXXEIVETEETNSADNVNVGNSITEEGEASGIILHKLSSSKI 187
V V Q + V T+ NS + +G + I HKL
Sbjct: 107 ---VNGVQQPASSQSDAMKQDKYVSTKPRNSKN----------DGVDTAIYHHKL----- 148
Query: 188 RCNDCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDG 245
R+ V + + D L+K S + I + A A+ES M ++
Sbjct: 149 ------RDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMNKVNNCDTNEA 193
Query: 246 PYKIKYRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
YK +YR + N+ NPD + K+ G + PE + AK++A
Sbjct: 194 AYKARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 237
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
Length = 114
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 7/99 (7%)
Query: 193 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDGPYKIK 250
+ +R++V AL V + E + + A A+ES M ++ YK +
Sbjct: 18 YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 72
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
YR + N+ NPD + K+ G + PE + AK++A
Sbjct: 73 YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 11/99 (11%)
Query: 193 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWGRSDGPYKIK 250
R+ V + + D L+K S + I + A A+ES M ++ YK +
Sbjct: 12 LRDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMNKVNNCDTNEAAYKAR 62
Query: 251 YRAVLGNLKDPKNPDFRRKVLFGQVKPETVVGMTAKEMA 289
YR + N+ NPD + K+ G + PE + AK++A
Sbjct: 63 YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 101
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
0.315 0.131 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,240,113
Number of Sequences: 62578
Number of extensions: 307072
Number of successful extensions: 650
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 642
Number of HSP's gapped (non-prelim): 10
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
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: 51 (24.3 bits)