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= 038232
(217 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 = 7e-10, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 42/70 (60%)
Query: 142 DSVRVAIALESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGM 201
D R++ +E +F D YK + ++ + NLKD KNPD RRNV G + P+ I M
Sbjct: 36 DCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVM 95
Query: 202 TAKEMAGDKM 211
T++EMA D++
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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/109 (32%), Positives = 62/109 (56%), Gaps = 5/109 (4%)
Query: 109 DCFREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPYKIK 168
D R+ VR + D L K +++ ++ +E A +VA +E +F + D YK K
Sbjct: 10 DQIRQSVRHSLKDILMKRLTDSNLKVPEEKAA----KVATKIEKELFSFFRDTDAKYKNK 65
Query: 169 YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGDKMLSCYQR 217
Y++++ NLKDPKN + V G+V P+ ++ M+ +E+A K L+ ++R
Sbjct: 66 YRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELAS-KELAAWRR 113
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 39/61 (63%)
Query: 150 LESAMFEKWDRYDGPYKIKYKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMAGD 209
+E A++++ D YK + ++ + NLKD KNP+ R+NV G + P+ MTA+EMA D
Sbjct: 48 IEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASD 107
Query: 210 K 210
+
Sbjct: 108 E 108
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 50/211 (23%), Positives = 86/211 (40%), Gaps = 32/211 (15%)
Query: 2 KASSRKKIQDFASDLIVSWRNMSLEQMRDERKGSYT---IPGDIEPAKIEKVDKRTSEEC 58
K S+ +I +I SW++ + R + + PG+ E DK T E
Sbjct: 54 KKSTNVEISKLVKKMISSWKDAINKNKRSRQAQQHHQDHAPGNAE-------DKTTVGES 106
Query: 59 QEISGVGIVKVQKVDQNATSLSSNVVRPESVVTEKTNSSDNLSRSMIRCNDCFREVVREK 118
V V Q A+S S + + + V T+ NS ++ + I + +R++
Sbjct: 107 ----------VNGVQQPASSQSDAMKQDKYVSTKPRNSKNDGVDTAI-----YHHKLRDQ 151
Query: 119 VCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWDRYDGPYKIKYKAVLGNL 176
V AL V + E + + A A+ES M D + YK +Y+ + N+
Sbjct: 152 VLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSNV 206
Query: 177 KDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
NPD + + G + PE + AK++A
Sbjct: 207 ISKNNPDLKHKIANGDITPEFLATCDAKDLA 237
>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 = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 111 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWDRYDGPYKIK 168
+ +R++V AL V + E + + A A+ES M D + YK +
Sbjct: 14 YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 68
Query: 169 YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
Y+ + N+ NPD + + G + PE + AK++A
Sbjct: 69 YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 107
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 111 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWDRYDGPYKIK 168
+ +R++V AL V + E + + A A+ES M D + YK +
Sbjct: 13 YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 67
Query: 169 YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
Y+ + N+ NPD + + G + PE + AK++A
Sbjct: 68 YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 106
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
Length = 114
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 111 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWDRYDGPYKIK 168
+ +R++V AL V + E + + A A+ES M D + YK +
Sbjct: 18 YHHKLRDQVLKALYDVLAKESEHPPQSI-----LHTAKAIESEMNKVNNCDTNEAAYKAR 72
Query: 169 YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
Y+ + N+ NPD + + 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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 11/99 (11%)
Query: 111 FREVVREKVCDALSKVSGEADEEIRDEVNACDSVRVAIALESAM--FEKWDRYDGPYKIK 168
R+ V + + D L+K S + I + A A+ES M D + YK +
Sbjct: 12 LRDQVLKALYDVLAKESEHPPQSI---------LHTAKAIESEMNKVNNCDTNEAAYKAR 62
Query: 169 YKAVLGNLKDPKNPDFRRNVHLGQVKPETIVGMTAKEMA 207
Y+ + N+ NPD + + G + PE + AK++A
Sbjct: 63 YRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 101
>pdb|1RFE|A Chain A, Crystal Structure Of Conserved Hypothetical Protein Rv2991
From Mycobacterium Tuberculosis
Length = 162
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 9/45 (20%)
Query: 121 DALSKVSGEADEEIRDEVNACDSVRVAIALESAMFEKWDRYDGPY 165
D L VS E EI +E A V V++ W+RY GPY
Sbjct: 81 DTLRGVSFEGVAEIVEEPEALHRVGVSV---------WERYTGPY 116
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
0.314 0.129 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,997,277
Number of Sequences: 62578
Number of extensions: 225420
Number of successful extensions: 401
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 375
Number of HSP's gapped (non-prelim): 32
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
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: 49 (23.5 bits)