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= 038233
(332 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DH3|A Chain A, Crystal Structure Of A Creb Bzip-Cre Complex Reveals The
Basis For Creb Faimly Selective Dimerization And Dna
Binding
pdb|1DH3|C Chain C, Crystal Structure Of A Creb Bzip-Cre Complex Reveals The
Basis For Creb Faimly Selective Dimerization And Dna
Binding
Length = 55
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/25 (64%), Positives = 21/25 (84%)
Query: 96 RLAQNREAARKSRLRKKAYVQQLES 120
RL +NREAAR+SR +KK YV+ LE+
Sbjct: 5 RLMKNREAARESRRKKKEYVKSLEN 29
>pdb|2DGC|A Chain A, Gcn4 Basic Domain, Leucine Zipper Complexed With AtfCREB
Site Dna
Length = 63
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 86 PKTPDPKTLRRLAQNREAARKSRLRKKAYVQQLES 120
P++ DP L+R A+N EAAR+SR RK ++QLE
Sbjct: 4 PESSDPAALKR-ARNTEAARRSRARKLQRMKQLED 37
>pdb|1DGC|A Chain A, The X-Ray Structure Of The Gcn4-Bzip Bound To AtfCREB SITE
Dna Shows The Complex Depends On Dna Flexibility
Length = 62
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 86 PKTPDPKTLRRLAQNREAARKSRLRKKAYVQQLES 120
P++ DP L+R A+N EAAR+SR RK ++QLE
Sbjct: 3 PESSDPAALKR-ARNTEAARRSRARKLQRMKQLED 36
>pdb|3RR1|A Chain A, Crystal Structure Of Enolase Prk14017 (Target Efi-500653)
From Ralstonia Pickettii 12j
pdb|3RR1|B Chain B, Crystal Structure Of Enolase Prk14017 (Target Efi-500653)
From Ralstonia Pickettii 12j
pdb|3RRA|A Chain A, Crystal Structure Of Enolase Prk14017 (Target Efi-500653)
From Ralstonia Pickettii 12j With Magnesium Bound
pdb|3RRA|B Chain B, Crystal Structure Of Enolase Prk14017 (Target Efi-500653)
From Ralstonia Pickettii 12j With Magnesium Bound
Length = 405
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 211 IMNLKGMVAKTDVFHLVSGLWKSPAERCFLWLGGFRPSELI 251
+ ++KG V V+ L+ GL + R + W+GG RP+++I
Sbjct: 91 LWDIKGKVLGVPVYELLGGLVRDKM-RTYSWVGGDRPADVI 130
>pdb|3OM3|B Chain B, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation In The
Reduced State
pdb|3OM3|D Chain D, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation In The
Reduced State
pdb|3OMA|B Chain B, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation
pdb|3OMA|D Chain D, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With K362m Mutation
pdb|3OMI|B Chain B, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation
pdb|3OMI|D Chain D, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation
pdb|3OMN|B Chain B, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation In The
Reduced State
pdb|3OMN|D Chain D, Catalytic Core Subunits (I And Ii) Of Cytochrome C Oxidase
From Rhodobacter Sphaeroides With D132a Mutation In The
Reduced State
Length = 256
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 14/59 (23%)
Query: 127 QLEQELQRARTQGMFFG------GILGGEQGLPVGISNISSEAAVFDMEYARWLEVHHR 179
+L Q RA +G+FFG GI +P+ + +S EA YA WLE HH
Sbjct: 205 RLAQLWFRAEREGIFFGQCSELCGI--SHAYMPITVKVVSEEA------YAAWLEQHHH 255
>pdb|1YSA|C Chain C, The Gcn4 Basic Region Leucine Zipper Binds Dna As A Dimer
Of Uninterrupted Alpha Helices: Crystal Structure Of The
Protein-Dna Complex
pdb|1YSA|D Chain D, The Gcn4 Basic Region Leucine Zipper Binds Dna As A Dimer
Of Uninterrupted Alpha Helices: Crystal Structure Of The
Protein-Dna Complex
Length = 58
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 89 PDPKTLRRLAQNREAARKSRLRKKAYVQQLESS 121
DP L+R A+N EAAR+SR RK ++QLE
Sbjct: 2 KDPAALKR-ARNTEAARRSRARKLQRMKQLEDK 33
>pdb|1LD4|E Chain E, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|F Chain F, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|G Chain G, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|H Chain H, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|I Chain I, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|J Chain J, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|K Chain K, Placement Of The Structural Proteins In Sindbis Virus
pdb|1LD4|L Chain L, Placement Of The Structural Proteins In Sindbis Virus
Length = 57
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/31 (54%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 90 DPKTLRRLAQNREAARKSRLRKKAYVQQLES 120
DP L+R A+N EAAR+SR RK ++QLE
Sbjct: 2 DPAALKR-ARNTEAARRSRARKLQRMKQLED 31
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 0.128 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,163,509
Number of Sequences: 62578
Number of extensions: 342010
Number of successful extensions: 652
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 644
Number of HSP's gapped (non-prelim): 12
length of query: 332
length of database: 14,973,337
effective HSP length: 99
effective length of query: 233
effective length of database: 8,778,115
effective search space: 2045300795
effective search space used: 2045300795
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: 52 (24.6 bits)