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= psy15634
(113 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 25/31 (80%), Positives = 28/31 (90%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 4 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 34
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 25/31 (80%), Positives = 28/31 (90%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 3 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 33
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1
And Sox2 Transcription Factors With A 19mer
Oligonucleotide From The Hoxb1 Regulatory Element
Length = 88
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 25/31 (80%), Positives = 28/31 (90%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 8 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 38
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 23/34 (67%), Positives = 29/34 (85%)
Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+ +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35
>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box
Domain Of The Human Male Sex Determining Factor Sry
Complexed To Dna
Length = 85
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/32 (71%), Positives = 28/32 (87%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 4 RVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35
>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr
pdb|1HRY|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multid-Dimensional Heteronuclear-Edited And-Filtered
Nmr
Length = 76
Score = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 23/32 (71%), Positives = 28/32 (87%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 4 RVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35
>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The
Hmg-Box Domain Of The Human Male Sex Determining Factor
Sry Complexed To Dna
Length = 85
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 22/32 (68%), Positives = 28/32 (87%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+KRP+NAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 4 RVKRPINAFIVWSRDQRRKMALENPRMRNSEI 35
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 51.6 bits (122), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 23/32 (71%), Positives = 27/32 (84%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
HIKRPMNAFMVWS+I+RRKI +P MHN+ I
Sbjct: 2 HIKRPMNAFMVWSQIERRKIMEQSPDMHNAEI 33
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/35 (65%), Positives = 26/35 (74%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
G HIKRPMNAFMVW++ +RRKI P MHNS I
Sbjct: 1 GSPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNI 35
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 27/35 (77%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
G I+RPMNAFMVW++ +R+++A NP +HN+ +
Sbjct: 4 GSSGIRRPMNAFMVWAKDERKRLAQQNPDLHNAEL 38
>pdb|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription
Factor Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS
AT 2.77 A RESOLUTION
Length = 106
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 18/32 (56%), Positives = 25/32 (78%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
H+KRPMNAFMVW++ RRK+A P +HN+ +
Sbjct: 29 HVKRPMNAFMVWAQAARRKLADQYPHLHNAEL 60
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 25/29 (86%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
I+RPMNAFMVW++ +R+++A NP +HN+
Sbjct: 3 IRRPMNAFMVWAKDERKRLAQQNPDLHNA 31
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 26/31 (83%)
Query: 30 IKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
I+RPMNAFMVW++ +R+++A NP +HN+ +
Sbjct: 7 IRRPMNAFMVWAKDERKRLAQQNPDLHNAEL 37
>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna
pdb|1QRV|B Chain B, Crystal Structure Of The Complex Of Hmg-D And Dna
Length = 73
Score = 28.5 bits (62), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKS 90
KRP++A+M+W R I +NP + + + + +K K + +A +
Sbjct: 5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRA-----MKDKSEWEAKAAKAK 59
Query: 91 NLFDR 95
+ +DR
Sbjct: 60 DDYDR 64
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 28.5 bits (62), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKS 90
KRP++A+M+W R I +NP + + + + +K K + +A +
Sbjct: 5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRA-----MKDKSEWEAKAAKAK 59
Query: 91 NLFDR 95
+ +DR
Sbjct: 60 DDYDR 64
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 28.5 bits (62), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 5/65 (7%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKS 90
KRP++A+M+W R I +NP + + + + +K K + +A +
Sbjct: 6 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRA-----MKDKSEWEAKAAKAK 60
Query: 91 NLFDR 95
+ +DR
Sbjct: 61 DDYDR 65
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
G + KRP++A ++S +RR++ + P++ S +
Sbjct: 17 GSEKPKRPVSAMFIFSEEKRRQLQEERPELSESEL 51
>pdb|3BXU|A Chain A, Ppcb, A Cytochrome C7 From Geobacter Sulfurreducens
pdb|3BXU|B Chain B, Ppcb, A Cytochrome C7 From Geobacter Sulfurreducens
Length = 71
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 54 KMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACR 88
K H +I+ +C + H P KIE K H ++C+
Sbjct: 18 KKHQTIVPDCAVCHGKTPGKIEGFGKEMAHGKSCK 52
>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex
pdb|3NM9|D Chain D, Hmgd(M13a)-Dna Complex
pdb|3NM9|G Chain G, Hmgd(M13a)-Dna Complex
pdb|3NM9|J Chain J, Hmgd(M13a)-Dna Complex
pdb|3NM9|M Chain M, Hmgd(M13a)-Dna Complex
pdb|3NM9|P Chain P, Hmgd(M13a)-Dna Complex
Length = 73
Score = 26.2 bits (56), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMHFLCPQKIELKSKRDIHVEACRKS 90
KRP++A+ +W R I +NP + + + + +K K + +A +
Sbjct: 5 KRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRA-----MKDKSEWEAKAAKAK 59
Query: 91 NLFDR 95
+ +DR
Sbjct: 60 DDYDR 64
>pdb|4DZ8|B Chain B, Human Igg1 Fc Fragment Heterodimer
Length = 207
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 17/60 (28%)
Query: 8 QHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSIIFNCHIMH 67
+++Y + PP LD+ +F ++SR K+ +D + +F+C +MH
Sbjct: 151 ENNYKTTPPVLDSD-------------GSFFLYSR----KLTVDKSRWQQGNVFSCSVMH 193
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHN 57
G +RPMNAF+++ + R + ++P++ N
Sbjct: 4 GSSGARRPMNAFLLFCKRHRSLVRQEHPRLDN 35
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
HIK+P+NAFM++ + R + ++ ++ I
Sbjct: 2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAI 33
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
0.325 0.135 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,371,899
Number of Sequences: 62578
Number of extensions: 117951
Number of successful extensions: 506
Number of sequences better than 100.0: 85
Number of HSP's better than 100.0 without gapping: 84
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 422
Number of HSP's gapped (non-prelim): 85
length of query: 113
length of database: 14,973,337
effective HSP length: 77
effective length of query: 36
effective length of database: 10,154,831
effective search space: 365573916
effective search space used: 365573916
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)