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= 025523
(251 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4H63|F Chain F, Structure Of The Schizosaccharomyces Pombe Mediator Head
Module
Length = 183
Score = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 49/141 (34%), Positives = 78/141 (55%), Gaps = 10/141 (7%)
Query: 24 DMTGICFRDQLWLNTYP-LDRNMIFDYFTLSLFYDRTCNNEQLRMRS-IHPLDI----SQ 77
D+T I +R W+ + L + +YF+ S FY NNE L+M+S + LD+ SQ
Sbjct: 13 DLTSIQWRMPEWVQSMGGLRTENVLEYFSQSPFYSHKSNNEMLKMQSQFNALDLGDLNSQ 72
Query: 78 LSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARI 137
L ++TGI++++ P L+VI+KQ R +V P+ Y+V + +IY AP + + R+
Sbjct: 73 LKRLTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRM 132
Query: 138 GRALHYIQKAFTTAASKLEKI 158
A + QKA T K+EK
Sbjct: 133 LNATYCFQKALT----KIEKF 149
>pdb|4H61|A Chain A, Structure Of The Schizosaccharomyces Pombe Mediator
Subunit Med6
pdb|4H61|B Chain B, Structure Of The Schizosaccharomyces Pombe Mediator
Subunit Med6
Length = 175
Score = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 49/141 (34%), Positives = 78/141 (55%), Gaps = 10/141 (7%)
Query: 24 DMTGICFRDQLWLNTYP-LDRNMIFDYFTLSLFYDRTCNNEQLRMRS-IHPLDI----SQ 77
D+T I +R W+ + L + +YF+ S FY NNE L+M+S + LD+ SQ
Sbjct: 5 DLTSIQWRMPEWVQSMGGLRTENVLEYFSQSPFYSHKSNNEMLKMQSQFNALDLGDLNSQ 64
Query: 78 LSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARI 137
L ++TGI++++ P L+VI+KQ R +V P+ Y+V + +IY AP + + R+
Sbjct: 65 LKRLTGIQFVIIHERPPFLWVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRM 124
Query: 138 GRALHYIQKAFTTAASKLEKI 158
A + QKA T K+EK
Sbjct: 125 LNATYCFQKALT----KIEKF 141
>pdb|4GWP|G Chain G, Structure Of The Mediator Head Module From S. Cerevisiae
pdb|4GWQ|G Chain G, Structure Of The Mediator Head Module From S. Cerevisiae
In Complex With The Carboxy-Terminal Domain (Ctd) Of Rna
Polymerase Ii Rpb1 Subunit
Length = 295
Score = 60.5 bits (145), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 42/160 (26%), Positives = 68/160 (42%), Gaps = 58/160 (36%)
Query: 35 WLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRM--------------------------- 67
W+ + L + DYF S F+D+T NN+ ++M
Sbjct: 16 WIQVFGLRTENVLDYFAESPFFDKTSNNQVIKMQRQFSQLNDPNAAVNMTQNIMTLPDGK 75
Query: 68 ---------------RSI---HPLDI---SQLSKMTGIEYMLSEVMEPHLFVIRKQKR-- 104
R I +P+ + +L K+ G EY+LS V EP +VIRKQ+R
Sbjct: 76 NGNLEEEFAYVDPARRQILFKYPMYMQLEEELMKLDGTEYVLSSVREPDFWVIRKQRRTN 135
Query: 105 -------DGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARI 137
GPE + P+ YY++ +IYQ+P + + +R+
Sbjct: 136 NSGVGSAKGPE-IIPLQDYYIIGANIYQSPTIFKIVQSRL 174
>pdb|3RJ1|G Chain G, Architecture Of The Mediator Head Module
pdb|3RJ1|N Chain N, Architecture Of The Mediator Head Module
pdb|3RJ1|U Chain U, Architecture Of The Mediator Head Module
Length = 295
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 10/81 (12%)
Query: 77 QLSKMTGIEYMLSEVMEPHLFVIRKQKR---------DGPEKVTPMLTYYVLDGSIYQAP 127
+L K+ G EY+LS V EP +VIRKQ+R GPE + P+ YY++ +IYQ+P
Sbjct: 106 ELXKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPE-IIPLQDYYIIGANIYQSP 164
Query: 128 QLCNVFSARIGRALHYIQKAF 148
+ + +R+ +++
Sbjct: 165 TIFKIVQSRLXSTSYHLNSTL 185
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 12/46 (26%), Positives = 25/46 (54%)
Query: 23 TDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMR 68
T + + ++ W+ + L + DYF S F+D+T NN+ ++ +
Sbjct: 4 TPLDELQWKSPEWIQVFGLRTENVLDYFAESPFFDKTSNNQVIKXQ 49
>pdb|1XEZ|A Chain A, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Pro-Toxin With Octylglucoside Bound
Length = 721
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 32 DQLWLNTYPLDRNMI 46
D LW+NTYP+D N I
Sbjct: 364 DALWVNTYPVDVNRI 378
>pdb|3O44|A Chain A, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|B Chain B, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|C Chain C, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|D Chain D, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|E Chain E, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|F Chain F, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|G Chain G, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|H Chain H, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|I Chain I, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|J Chain J, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|K Chain K, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|L Chain L, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|M Chain M, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
pdb|3O44|N Chain N, Crystal Structure Of The Vibrio Cholerae Cytolysin (Hlya)
Heptameric Pore
Length = 593
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 32 DQLWLNTYPLDRNMI 46
D LW+NTYP+D N I
Sbjct: 236 DALWVNTYPVDVNRI 250
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
0.321 0.135 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,193,204
Number of Sequences: 62578
Number of extensions: 189618
Number of successful extensions: 418
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 406
Number of HSP's gapped (non-prelim): 9
length of query: 251
length of database: 14,973,337
effective HSP length: 96
effective length of query: 155
effective length of database: 8,965,849
effective search space: 1389706595
effective search space used: 1389706595
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)