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= psy5107
(74 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 32/38 (84%), Positives = 33/38 (86%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
HIKRPMNAFMVWSQ+ERRKI E PDMHNAEISKRL
Sbjct: 1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLG 38
>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 = 59.7 bits (143), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 25/39 (64%), Positives = 32/39 (82%)
Query: 15 PNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
P+ +KRPMNAFMVWS+ +RRK+ + P MHN+EISKRL
Sbjct: 5 PDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 43
>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 = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 27/46 (58%), Positives = 34/46 (73%), Gaps = 1/46 (2%)
Query: 10 TKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
+ KN P H+KRPMNAFMVW+Q RRK+ + P +HNAE+SK L L
Sbjct: 23 SSKNKP-HVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKL 67
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 26/37 (70%), Positives = 30/37 (81%)
Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
HIKRPMNAFMVW++ ERRKI + PDMHN+ ISK L
Sbjct: 4 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILG 40
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 24/38 (63%), Positives = 31/38 (81%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
+ +KRPMNAFMVWS+ +RRK+ + P MHN+EISKRL
Sbjct: 2 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 39
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 24/38 (63%), Positives = 31/38 (81%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
+ +KRPMNAFMVWS+ +RRK+ + P MHN+EISKRL
Sbjct: 1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 38
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 30/36 (83%)
Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
I+RPMNAFMVW++ ER+++ + PD+HNAE+SK L
Sbjct: 8 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLG 43
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 30/36 (83%)
Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
I+RPMNAFMVW++ ER+++ + PD+HNAE+SK L
Sbjct: 3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLG 38
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 30/36 (83%)
Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
I+RPMNAFMVW++ ER+++ + PD+HNAE+SK L
Sbjct: 7 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLG 42
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/38 (55%), Positives = 29/38 (76%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
+ +KRPMNAF+VWS+ +RRK+ P M N+EISK+L
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
+PN KRP +AF ++ R KI P + +++K+L +
Sbjct: 85 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEM 126
>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 = 1e-06, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 33/52 (63%), Gaps = 9/52 (17%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLL 67
+ +KRPMNAF+VWS+ +RRK+ P M N+EISK+L G+ W +
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQL---------GYQWKM 45
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 21/38 (55%), Positives = 29/38 (76%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
+ +KRPMNAF+VWS+ +RRK+ P M N+EISK+L
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40
>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 = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 9/52 (17%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNWLL 67
+ +KRP+NAF+VWS+ +RRK+ P M N+EISK+L G+ W +
Sbjct: 3 DRVKRPINAFIVWSRDQRRKMALENPRMRNSEISKQL---------GYQWKM 45
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 31/50 (62%)
Query: 6 PMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
P + K KRP++A ++S+ +RR++ E +P++ +E+++ LA +
Sbjct: 9 PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARM 58
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 33.1 bits (74), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 13 NNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEIS 49
+PN KRPMNAFM++++ R + ++ P N IS
Sbjct: 13 TSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAIS 49
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
KK +PN KRP +AF ++ R KI P + + +K+L +
Sbjct: 2 KKKDPNAPKRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEM 46
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 29.6 bits (65), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 1 MGLYSPMRA-TKKN--NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
M Y P + TKK +PN KRP +AF ++ R KI P + +++K+L +
Sbjct: 82 MKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEM 139
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 29.6 bits (65), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 23/44 (52%)
Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
K +PN KRP +AF ++ R KI P + + +K+L +
Sbjct: 2 KKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEM 45
>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
pdb|1HMF|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
Length = 77
Score = 29.3 bits (64), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
+PN KRP +AF ++ R KI P + +++K+L
Sbjct: 3 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLG 42
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
KRP++A+M+W R I P + E++KR L
Sbjct: 6 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGEL 42
>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 = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
KRP++A+M+W R I P + E++KR L
Sbjct: 5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGEL 41
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 28.9 bits (63), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
KRP++A+M+W R I P + E++KR L
Sbjct: 5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGEL 41
>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 = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALL 55
KRP++A+ +W R I P + E++KR L
Sbjct: 5 KRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGEL 41
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
+PN KR ++A+M ++ R + PD+ ++ K+L
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLG 56
>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb
Protein Nhp6a In Complex With Sry Dna
pdb|1LWM|A Chain A, Solution Structure Of The Sequence-Non-Specific Hmgb
Protein Nhp6a
Length = 93
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 14 NPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
+PN KR ++A+M ++ R + PD+ ++ K+L
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLG 56
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
+RPMNAF+++ + R + + P + N +K LA
Sbjct: 9 RRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILA 43
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human
Upstream Binding Factor
Length = 99
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 25/42 (59%)
Query: 12 KNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
K +P+ K+P+ + + +R K ++ P+M N +++K L+
Sbjct: 5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILS 46
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
0.322 0.132 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,082,866
Number of Sequences: 62578
Number of extensions: 57154
Number of successful extensions: 132
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 103
Number of HSP's gapped (non-prelim): 29
length of query: 74
length of database: 14,973,337
effective HSP length: 44
effective length of query: 30
effective length of database: 12,219,905
effective search space: 366597150
effective search space used: 366597150
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)