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= psy6707
(257 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 33/42 (78%), Positives = 40/42 (95%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRT 184
G+RWKAM+N EKQPYYEEQ+RLSK H+EK+PDY+Y+PRPKRT
Sbjct: 40 GSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKPRPKRT 81
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 40/73 (54%), Gaps = 11/73 (15%)
Query: 124 VWGAGGESPYKMPEETPDK---------GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPD 174
VW G KM +E P GA WK +S EK+P+ +E RL LHM++HPD
Sbjct: 17 VWSRGQRR--KMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPD 74
Query: 175 YRYRPRPKRTCIV 187
Y+YRPR K ++
Sbjct: 75 YKYRPRRKTKTLM 87
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 38/68 (55%), Gaps = 11/68 (16%)
Query: 124 VWGAGGESPYKMPEETPDK---------GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPD 174
VW G KM +E P GA WK +S EK+P+ +E RL LHM++HPD
Sbjct: 13 VWSRGQRR--KMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPD 70
Query: 175 YRYRPRPK 182
Y+YRPR K
Sbjct: 71 YKYRPRRK 78
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 38/68 (55%), Gaps = 11/68 (16%)
Query: 124 VWGAGGESPYKMPEETPDK---------GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPD 174
VW G KM +E P GA WK +S EK+P+ +E RL LHM++HPD
Sbjct: 12 VWSRGQRR--KMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPD 69
Query: 175 YRYRPRPK 182
Y+YRPR K
Sbjct: 70 YKYRPRRK 77
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/38 (55%), Positives = 28/38 (73%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPR 180
G WKA++ AEK+P+ EE RL HM+ HP+Y+YRPR
Sbjct: 42 GKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRPR 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 = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 30/40 (75%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPK 182
G +WK ++ AEK P+++E +L +H EK+P+Y+YRPR K
Sbjct: 40 GYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRK 79
>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 = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 30/40 (75%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPK 182
G +WK ++ AEK P+++E +L +H EK+P+Y+YRPR K
Sbjct: 40 GYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRK 79
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 9/58 (15%)
Query: 134 KMPEETPDK---------GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPK 182
K+ E++PD G RWK + +++K P+ +E RL HM +PDY+YRPR K
Sbjct: 20 KIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYRPRKK 77
>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 = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 28/37 (75%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRP 179
G +WK ++ AEK P+++E +L +H EK+P+Y+YRP
Sbjct: 40 GYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP 76
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 27/36 (75%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYR 178
G +WK ++ AEK P+++E +L +H EK+P+Y+YR
Sbjct: 40 GYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/37 (48%), Positives = 25/37 (67%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRP 179
G WKA++ AEK+P+ EE RL HM+ HP+Y+ P
Sbjct: 43 GKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKSGP 79
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 29/42 (69%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRT 184
G W+ ++ +EK+P+ EE RL H + HPDY+Y+PR +++
Sbjct: 65 GKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRRRKS 106
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 24/34 (70%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYR 176
G WKA++ AEK+P+ EE RL HM+ HP+Y+
Sbjct: 38 GKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK 71
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYR 178
G RW A+S E+ YYE + +LHM+ +P + R
Sbjct: 38 GRRWHALSREEQAKYYELARKERQLHMQLYPGWSAR 73
>pdb|3TIX|B Chain B, Crystal Structure Of The Chp1-Tas3 Complex Core
pdb|3TIX|D Chain D, Crystal Structure Of The Chp1-Tas3 Complex Core
Length = 458
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 115 SEEQDLLMSVWGAGGES--PYKMPEETPDKG--ARWKAMSNAEKQPYYEEQSRLSKLHME 170
+E+ + LM+++ G+S P+ M P + W A + K+PY++ QS LS L
Sbjct: 121 TEDNNALMNLYDCQGQSNSPFWMVIFEPLESILVEWSAKNLRPKKPYHKSQSYLSYLLQL 180
Query: 171 KHPD 174
H D
Sbjct: 181 GHID 184
>pdb|4EJO|A Chain A, Crystal Structure Of Padr Family Transcriptional Regulator
From Eggerthella Lenta Dsm 2243
pdb|4EJO|B Chain B, Crystal Structure Of Padr Family Transcriptional Regulator
From Eggerthella Lenta Dsm 2243
Length = 123
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 102 PHDKNMYSPHHDKSEEQDLLMSVWGAGGESPYKMPEETPDKGAR 145
P + N P + E Q LL S W GG P K T D+G R
Sbjct: 49 PIEANTLYPLXRRLESQGLLASEWDNGGSKPRKY-YRTTDEGLR 91
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 0.128 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,520,888
Number of Sequences: 62578
Number of extensions: 280179
Number of successful extensions: 542
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 524
Number of HSP's gapped (non-prelim): 23
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
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)