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= psy2693
(122 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MKR|B Chain B, Crystal Structure Of Yeast AlphaEPSILON-Cop Subcomplex Of
The Copi Vesicular Coat
Length = 320
Score = 92.0 bits (227), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 42/84 (50%), Positives = 56/84 (66%), Gaps = 2/84 (2%)
Query: 12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
VA Q RK+L+ C NPTD + ++YD HNPF ICA SY PIY G+ E C GA Y P++
Sbjct: 233 VAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 292
Query: 72 KGELCAVCTVSVIDTHRNAYGLQI 95
KG++C V TV+ I ++ GL+I
Sbjct: 293 KGQICKVTTVTEIG--KDVIGLRI 314
>pdb|3MV3|A Chain A, Crystal Structure Of A-Cop In Complex With E-Cop
pdb|3MV3|C Chain C, Crystal Structure Of A-Cop In Complex With E-Cop
pdb|3MV3|E Chain E, Crystal Structure Of A-Cop In Complex With E-Cop
Length = 325
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 11 PVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPK 70
P A QARK+ ++ +D ID+D + F ICA +Y PIY S + G+ Y+
Sbjct: 241 PRAEQARKIKNKADSXASDAIPIDFDPYAKFDICAATYKPIYEDTPSVSDPLTGSKYVIT 300
Query: 71 YKGELCAVCTVSVIDTHRNAYGLQI 95
K ++ + +S I A GL+I
Sbjct: 301 EKDKIDRIAXISKIGAP--ASGLRI 323
>pdb|3MV2|A Chain A, Crystal Structure Of A-Cop In Complex With E-Cop
pdb|3MV2|C Chain C, Crystal Structure Of A-Cop In Complex With E-Cop
pdb|3MV2|E Chain E, Crystal Structure Of A-Cop In Complex With E-Cop
Length = 325
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 11 PVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPK 70
P A QARK+ ++ +D ID+D + F ICA +Y PIY S + G+ Y+
Sbjct: 241 PRAEQARKIKNKADSMASDAIPIDFDPYAKFDICAATYKPIYEDTPSVSDPLTGSKYVIT 300
Query: 71 YKGELCAVCTVSVIDTHRNAYGLQI 95
K ++ + +S I A GL+I
Sbjct: 301 EKDKIDRIAMISKIGAP--ASGLRI 323
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 32 TIDYDEHNPFQ---ICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDT 86
TI+Y P + CAR + P+ + C+ CG K++G +C C V V T
Sbjct: 43 TINYRTFKPERDGLFCARIFGPV----KDYECL-CGKYKRLKHRGVICEKCGVEVTQT 95
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 32 TIDYDEHNPFQ---ICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDT 86
TI+Y P + CAR + P+ + C+ CG K++G +C C V V T
Sbjct: 43 TINYRTFKPERDGLFCARIFGPV----KDYECL-CGKYKRLKHRGVICEKCGVEVTQT 95
>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna
Binding Complex
pdb|1R0O|B Chain B, Crystal Structure Of The Heterodimeric Ecdysone Receptor
Dna-Binding Complex
Length = 109
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 69 PKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINN 107
P+ + ELC VC H NA + C G + V +
Sbjct: 2 PRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKS 40
>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor
Interaction With Natural Response Element Hsp27 Gene
Promoter
Length = 119
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 69 PKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINN 107
P+ + ELC VC H NA + C G + V +
Sbjct: 4 PRVQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKS 42
>pdb|2FF0|A Chain A, Solution Structure Of Steroidogenic Factor 1 Dna Binding
Domain Bound To Its Target Sequence In The Inhibin
Alpha- Subunit Promoter
Length = 102
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 14/34 (41%)
Query: 74 ELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINN 107
ELC VC V H + C G K V NN
Sbjct: 2 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNN 35
>pdb|2A66|A Chain A, Human Liver Receptor Homologue Dna-Binding Domain (Hlrh-1
Dbd) In Complex With Dsdna From The Hcyp7a1 Promoter
Length = 113
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 14/34 (41%)
Query: 74 ELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINN 107
ELC VC V H + C G K V NN
Sbjct: 10 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNN 43
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
0.322 0.134 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,657,566
Number of Sequences: 62578
Number of extensions: 138617
Number of successful extensions: 191
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 183
Number of HSP's gapped (non-prelim): 9
length of query: 122
length of database: 14,973,337
effective HSP length: 84
effective length of query: 38
effective length of database: 9,716,785
effective search space: 369237830
effective search space used: 369237830
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)