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= psy15631
(213 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 = 69.3 bits (168), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 31/33 (93%), Positives = 32/33 (96%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 49 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 81
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 31/33 (93%), Positives = 32/33 (96%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 48 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 80
>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 = 68.9 bits (167), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 31/33 (93%), Positives = 32/33 (96%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKT 34
EKRPFIDEAKRLRA+HMKEHPDYKYRPRRK KT
Sbjct: 53 EKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT 85
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 21/32 (65%), Positives = 29/32 (90%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
EKRPF++EA+RLR HM++HP+YKYRPRR+ +
Sbjct: 52 EKRPFVEEAERLRVQHMQDHPNYKYRPRRRKQ 83
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 21/30 (70%), Positives = 27/30 (90%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRK 31
EKRPF++EA+RLR H K+HPDYKY+PRR+
Sbjct: 75 EKRPFVEEAERLRVQHKKDHPDYKYQPRRR 104
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/32 (65%), Positives = 26/32 (81%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
+K PFI EA+RLR HM ++PDYKYRPR+K K
Sbjct: 48 DKIPFIQEAERLRLKHMADYPDYKYRPRKKVK 79
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/32 (62%), Positives = 27/32 (84%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
EK PF EA++L+AMH +++P+YKYRPRRK K
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAK 81
>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 = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/32 (62%), Positives = 27/32 (84%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPK 33
EK PF EA++L+AMH +++P+YKYRPRRK K
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRPRRKAK 81
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 17/27 (62%), Positives = 23/27 (85%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRP 28
EKRPF++EA+RLR HM++HP+YK P
Sbjct: 53 EKRPFVEEAERLRVQHMQDHPNYKSGP 79
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/24 (66%), Positives = 22/24 (91%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYK 25
EKRPF++EA+RLR HM++HP+YK
Sbjct: 48 EKRPFVEEAERLRVQHMQDHPNYK 71
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/27 (59%), Positives = 23/27 (85%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRP 28
EK PF EA++L+AMH +++P+YKYRP
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYRP 76
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 28/45 (62%), Gaps = 7/45 (15%)
Query: 2 EKRPFIDEAKRLRAMHMKEHPDYKYRPRRKPKTPGQSIPNNKSPN 46
EK PF EA++L+AMH +++P+YKYR G++ K PN
Sbjct: 50 EKWPFFQEAQKLQAMHREKYPNYKYR-------KGETKKKFKDPN 87
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 23/29 (79%)
Query: 1 MEKRPFIDEAKRLRAMHMKEHPDYKYRPR 29
+EK+P+ +E RL H++++PDYKY+PR
Sbjct: 49 LEKQPYYEEQARLSKQHLEKYPDYKYKPR 77
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
0.315 0.131 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,632,306
Number of Sequences: 62578
Number of extensions: 201791
Number of successful extensions: 380
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 366
Number of HSP's gapped (non-prelim): 14
length of query: 213
length of database: 14,973,337
effective HSP length: 95
effective length of query: 118
effective length of database: 9,028,427
effective search space: 1065354386
effective search space used: 1065354386
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)