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= psy14051
(256 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 108 bits (270), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 59/108 (54%), Positives = 67/108 (62%), Gaps = 34/108 (31%)
Query: 5 INLDEIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIAS 64
IN +EI+EFAK FK+RRLSLGLTQTQVGQA + TEGPAYSQSAI
Sbjct: 1 INXEEIREFAKNFKIRRLSLGLTQTQVGQAXTATEGPAYSQSAI---------------- 44
Query: 65 XXXXXXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAEER 112
+ FEKLDITPKSAQK+KPVLE+W+ EAE R
Sbjct: 45 ------------------SRFEKLDITPKSAQKLKPVLEKWLNEAELR 74
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/102 (31%), Positives = 50/102 (49%), Gaps = 34/102 (33%)
Query: 10 IKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASXXXXX 69
+++FA FK+RR+ LG TQT VG+AL+ G +SQ+ IC
Sbjct: 5 LEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICR------------------- 45
Query: 70 XXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAEE 111
FE L ++ K+A K+K +L +W++EAE+
Sbjct: 46 ---------------FENLQLSFKNACKLKAILSKWLEEAEQ 72
>pdb|1POU|A Chain A, The Solution Structure Of The Oct-1 Pou-Specific Domain
Reveals A Striking Similarity To The Bacteriophage
Lambda Repressor Dna-Binding Domain
Length = 71
Score = 55.1 bits (131), Expect = 4e-08, Method: Composition-based stats.
Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 34/105 (32%)
Query: 6 NLDEIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASX 65
+L+E+++FAK FK RR+ LG TQ VG A+ G +SQ+ I
Sbjct: 1 DLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTI----------------- 43
Query: 66 XXXXXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAE 110
+ FE L+++ K+ K+KP+LE+W+ +AE
Sbjct: 44 -----------------SRFEALNLSFKNMCKLKPLLEKWLNDAE 71
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 55.1 bits (131), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 50/105 (47%), Gaps = 34/105 (32%)
Query: 6 NLDEIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASX 65
+L+E+++FAK FK RR+ LG TQ VG A+ G +SQ+ I
Sbjct: 5 DLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISR--------------- 49
Query: 66 XXXXXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAE 110
FE L+++ K+ K+KP+LE+W+ +AE
Sbjct: 50 -------------------FEALNLSFKNMSKLKPLLEKWLNDAE 75
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 34/105 (32%)
Query: 6 NLDEIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASX 65
+L+E+++FAK FK RR+ LG TQ VG A+ G +SQ+ I
Sbjct: 5 DLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTI----------------- 47
Query: 66 XXXXXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAE 110
+ FE L+++ K+ K+KP+LE+W+ +AE
Sbjct: 48 -----------------SRFEALNLSFKNMSKLKPLLEKWLNDAE 75
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 34/105 (32%)
Query: 6 NLDEIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASX 65
+L+E+++FAK FK RR+ LG TQ VG A+ G +SQ+ I
Sbjct: 9 DLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTI----------------- 51
Query: 66 XXXXXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAE 110
+ FE L+++ K+ K+KP+LE+W+ +AE
Sbjct: 52 -----------------SRFEALNLSFKNMAKLKPLLEKWLNDAE 79
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 47/103 (45%), Gaps = 34/103 (33%)
Query: 8 DEIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASXXX 67
D++++FAK FK RR+ LG TQ VG AL G +SQ+ IC
Sbjct: 13 DDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICR----------------- 55
Query: 68 XXXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAE 110
FE L ++ K+ K+KP+L +W++E +
Sbjct: 56 -----------------FEALQLSFKNMCKLKPLLNKWLEETD 81
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 34/105 (32%)
Query: 6 NLDEIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASX 65
+L+E+++FAK FK RR+ LG TQ VG A+ G +SQ+ I
Sbjct: 1 DLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTI----------------- 43
Query: 66 XXXXXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAE 110
+ FE L+++ K+ K+KP+LE+W+ +AE
Sbjct: 44 -----------------SRFEALNLSFKNMCKLKPLLEKWLNDAE 71
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 51/105 (48%), Gaps = 34/105 (32%)
Query: 6 NLDEIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASX 65
+L+E+++FAK FK RR+ LG TQ VG A+ G +SQ+ I
Sbjct: 8 DLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTI----------------- 50
Query: 66 XXXXXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAE 110
+ FE L+++ K+ K+KP+LE+W+ +AE
Sbjct: 51 -----------------SRFEALNLSFKNMCKLKPLLEKWLNDAE 78
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 34/102 (33%)
Query: 9 EIKEFAKAFKLRRLSLGLTQTQVGQALSVTEGPAYSQSAICSALATQMLCAAQIASXXXX 68
E+++FAK K +R++LG TQ VG L V G +SQ+ I
Sbjct: 11 ELEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISR------------------ 52
Query: 69 XXXXXXXXXXXXXNTMFEKLDITPKSAQKIKPVLERWMKEAE 110
FE L ++ K+ K++P+LE+W++EA+
Sbjct: 53 ----------------FEALQLSLKNMSKLRPLLEKWVEEAD 78
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
0.313 0.127 0.354
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,213,699
Number of Sequences: 62578
Number of extensions: 136325
Number of successful extensions: 322
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 302
Number of HSP's gapped (non-prelim): 20
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
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: 50 (23.9 bits)