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= 028123
(213 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MGU|A Chain A, Saccharomyces Cerevisiae Tpa1
Length = 644
Score = 31.6 bits (70), Expect = 0.31, Method: Composition-based stats.
Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 5/99 (5%)
Query: 105 HAKALMPSFGDGKEDQHAIESLTQEITNILKRSEKRLQQLSAAGPSEDSNVRKNVQRSLA 164
H + ++ K D ES+T I++ +K SE LS E + K +++
Sbjct: 299 HFEKMLKGDAGAKTDNTPKESMTSVISDSVKLSEAEFTYLSQYISPEHLS-SKGIEKLQK 357
Query: 165 TDLQNLSME----LRKKQSTYLKRLRQQKEVHEEFPCRS 199
++N S++ L +S LK++ +QKE+ +E P S
Sbjct: 358 QFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHS 396
>pdb|3KT7|A Chain A, Crystal Structure Of Tpa1 From Saccharomyces Cerevisiae, A
Component Of The Messenger Ribonucleoprotein Complex
Length = 633
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 5/99 (5%)
Query: 105 HAKALMPSFGDGKEDQHAIESLTQEITNILKRSEKRLQQLSAAGPSEDSNVRKNVQRSLA 164
H + ++ K D ES+T I++ +K SE LS E + K +++
Sbjct: 280 HFEKMLKGDAGAKTDNTPKESMTSVISDSVKLSEAEFTYLSQYISPEHLS-SKGIEKLQK 338
Query: 165 TDLQNLSME----LRKKQSTYLKRLRQQKEVHEEFPCRS 199
++N S++ L +S LK++ +QKE+ +E P S
Sbjct: 339 QFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHS 377
>pdb|3KT1|A Chain A, Crystal Structure Of Tpa1 From Saccharomyces Cerevisiae, A
Component Of The Messenger Ribonucleoprotein Complex
Length = 633
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 5/99 (5%)
Query: 105 HAKALMPSFGDGKEDQHAIESLTQEITNILKRSEKRLQQLSAAGPSEDSNVRKNVQRSLA 164
H + ++ K D ES+T I++ +K SE LS E + K +++
Sbjct: 280 HFEKMLKGDAGAKTDNTPKESMTSVISDSVKLSEAEFTYLSQYISPEHLS-SKGIEKLQK 338
Query: 165 TDLQNLSME----LRKKQSTYLKRLRQQKEVHEEFPCRS 199
++N S++ L +S LK++ +QKE+ +E P S
Sbjct: 339 QFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHS 377
>pdb|1CDW|A Chain A, Human Tbp Core Domain Complexed With Dna
Length = 179
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 1 MATRNRTLIY--KRYRDALKTVRVPTSTSPLQSSGKSSCSG 39
+A R R Y KR+ + +R P +T+ + SSGK C+G
Sbjct: 25 IALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTG 65
>pdb|1C9B|B Chain B, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|F Chain F, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|J Chain J, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|N Chain N, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|R Chain R, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
Length = 180
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 1 MATRNRTLIY--KRYRDALKTVRVPTSTSPLQSSGKSSCSG 39
+A R R Y KR+ + +R P +T+ + SSGK C+G
Sbjct: 26 IALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTG 66
>pdb|1NVP|A Chain A, Human TfiiaTBPDNA COMPLEX
Length = 181
Score = 28.1 bits (61), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 1 MATRNRTLIY--KRYRDALKTVRVPTSTSPLQSSGKSSCSG 39
+A R R Y KR+ + +R P +T+ + SSGK C+G
Sbjct: 25 IALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTG 65
>pdb|1JFI|C Chain C, Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
Length = 185
Score = 28.1 bits (61), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 1 MATRNRTLIY--KRYRDALKTVRVPTSTSPLQSSGKSSCSG 39
+A R R Y KR+ + +R P +T+ + SSGK C+G
Sbjct: 29 IALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTG 69
>pdb|1TGH|A Chain A, Tata Binding Protein (Tbp)DNA COMPLEX
Length = 185
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 1 MATRNRTLIY--KRYRDALKTVRVPTSTSPLQSSGKSSCSG 39
+A R R Y KR+ + +R P +T+ + SSGK C+G
Sbjct: 29 IALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTG 69
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
0.312 0.126 0.346
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,366,448
Number of Sequences: 62578
Number of extensions: 184372
Number of successful extensions: 426
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 421
Number of HSP's gapped (non-prelim): 16
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)