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= psy7578
(280 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 37/57 (64%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
A+M+WAK R++L + NP++ +++SK LG+ W + EK + +A+RL ++ Q
Sbjct: 13 AFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQ 69
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 37/59 (62%)
Query: 77 FTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
A+M+WAK R++L + NP++ +++SK LG+ W + EK + +A+RL ++ Q
Sbjct: 12 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQ 70
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 37/59 (62%)
Query: 77 FTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
A+M+WAK R++L + NP++ +++SK LG+ W + EK + +A+RL ++ Q
Sbjct: 7 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQ 65
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 38/63 (60%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K A+++W++ R+K+ NP M S++SK+LG W + EK+ + ++A +L A +
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65
Query: 134 TQK 136
+K
Sbjct: 66 REK 68
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 49/82 (59%), Gaps = 7/82 (8%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K A+M+W++ R+K+++ +P+M +++SK+LG+ W + ++K + ++A+RL K+
Sbjct: 4 KRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKH 63
Query: 134 TQKMSKAPAQKTKSTYTPHGRV 155
M+ P K Y P +V
Sbjct: 64 ---MADYPDYK----YRPRKKV 78
>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 = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 38/63 (60%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K A+++W++ R+K+ NP M S++SK+LG W + EK+ + ++A +L A +
Sbjct: 6 KRPINAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65
Query: 134 TQK 136
+K
Sbjct: 66 REK 68
>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 = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 38/63 (60%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K A+++W++ R+K+ NP M S++SK+LG W + EK+ + ++A +L A +
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH 65
Query: 134 TQK 136
+K
Sbjct: 66 REK 68
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEK--YGWKRQADR 128
K +AYM +A + R + NP++ F QV KKLGE W + EK Y K QAD+
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADK 78
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEK--YGWKRQADR 128
K +AYM +A + R + NP++ F QV KKLGE W + EK Y K QAD+
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADK 78
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 77 FTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+W++ R+K+ + NP+M S++SK+LG W + EK + +A RL A + ++
Sbjct: 12 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 71
Query: 137 ---MSKAPAQKTKS 147
P +KTK+
Sbjct: 72 HPDYKYRPRRKTKT 85
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 77 FTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+W++ R+K+ + NP+M S++SK+LG W + EK + +A RL A + ++
Sbjct: 8 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 67
Query: 137 ---MSKAPAQKTKS 147
P +KTK+
Sbjct: 68 HPDYKYRPRRKTKT 81
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 3/74 (4%)
Query: 77 FTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+W++ R+K+ + NP+M S++SK+LG W + EK + +A RL A + ++
Sbjct: 7 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 66
Query: 137 ---MSKAPAQKTKS 147
P +KTK+
Sbjct: 67 HPDYKYRPRRKTKT 80
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
A+++W++ R+K+ NP M S++SK+LG W + EK+ + ++A +L A + +K
Sbjct: 10 NAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY 69
Query: 138 SKAPAQK--TKSTYTPHGRVGRPP 159
+K TK + RPP
Sbjct: 70 PNYKYRKGETKKKFKDPNAPKRPP 93
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEK 119
+A+ L+ + R K+ +P + V+KKLGE+W+ ++K
Sbjct: 94 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDK 135
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 36/61 (59%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+ + L+ + R K+ +NP + V+KKLGE+W+ + +EK + +A +L KY + +
Sbjct: 15 SGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDV 74
Query: 138 S 138
+
Sbjct: 75 A 75
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K +AYMLW R+ + + NP + ++V+K+ GELW + +K W+ +A + Y
Sbjct: 5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAKDDY 62
Query: 134 TQKMSKAPA 142
+ + + A
Sbjct: 63 DRAVKEFEA 71
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 36/58 (62%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
A+M+WA+ R+KL P + +++SK LG+LW + +EK + +A+RL ++ +
Sbjct: 35 NAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKK 92
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 36/59 (61%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+WAK R+K++++ P+M S +SK LG W + EK + + RL+ ++ +K
Sbjct: 10 NAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 68
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 77 FTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
+AYMLW R+ + + NP + ++V+K+ GELW + +K W+ +A + Y +
Sbjct: 9 LSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAKDDYDR 65
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 77 FTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
+AYMLW R+ + + NP + ++V+K+ GELW + +K W+ +A + Y +
Sbjct: 8 LSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAKDDYDR 64
>pdb|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like
Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A)
Length = 97
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 77 FTAYMLWAKQIRQKLIKSNPEM--DFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYT 134
++YM +AK+ R ++I NPE+ D + + K +G W+ + EK ++R +D +Y
Sbjct: 27 LSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYE 86
Query: 135 QKMSKAPAQKT 145
++ ++ +K
Sbjct: 87 REKAEYAQRKV 97
>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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K +AY LW R+ + + NP + ++V+K+ GELW + +K W+ +A + Y
Sbjct: 5 KRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAKDDY 62
Query: 134 TQKMSKAPA 142
+ + + A
Sbjct: 63 DRAVKEFEA 71
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
TA+MLW R+ + + NP + ++++KK GE+W + +K W+ A + +Y +M
Sbjct: 9 TAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEM 66
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 35.8 bits (81), Expect = 0.026, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 78 TAYMLWAKQIRQKLIKSNPEM--DFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
+AY + + R++ K NPE+ +F++ SKK E W T+ EK + A +Y +
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 136 KM 137
+M
Sbjct: 81 EM 82
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 35.8 bits (81), Expect = 0.030, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPE--MDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAA 131
+ + ++Y + + R++ K +P+ ++FS+ SKK E W T+ EK ++ A A
Sbjct: 3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 62
Query: 132 KYTQKM 137
+Y ++M
Sbjct: 63 RYEREM 68
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 35.4 bits (80), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 4/90 (4%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPE--MDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAA 131
+ + ++Y + + R++ K +P+ ++FS+ SKK E W T+ EK ++ A A
Sbjct: 17 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 76
Query: 132 KYTQKMSK--APAQKTKSTYTPHGRVGRPP 159
+Y ++M P +TK + RPP
Sbjct: 77 RYEREMKTYIPPKGETKKKFKDPNAPKRPP 106
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEK 119
+A+ L+ + R K+ +P + V+KKLGE+W+ ++K
Sbjct: 107 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDK 148
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 34.7 bits (78), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 32/58 (55%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
+A+ L+ + R K+ +P + +KKLGE+W +K ++++A +L KY +
Sbjct: 14 SAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEK 71
>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53
Transactivation Domain Interaction And Is Regulated By
The Acidic Tail
Length = 83
Score = 34.7 bits (78), Expect = 0.064, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPE--MDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAA 131
+ + ++Y + + R++ K +P+ ++FS+ SKK E W T+ EK ++ A A
Sbjct: 9 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 68
Query: 132 KYTQKM 137
+Y ++M
Sbjct: 69 RYEREM 74
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 34.3 bits (77), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 32/58 (55%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
+A+ L+ + R K+ +P + +KKLGE+W +K ++++A +L KY +
Sbjct: 13 SAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEK 70
>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
pdb|1NHN|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
Length = 81
Score = 34.3 bits (77), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEK 119
+A+ L+ + R K+ +P + V+KKLGE+W+ ++K
Sbjct: 10 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDK 51
>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
pdb|1HSN|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
Length = 79
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEK 119
+A+ L+ + R K+ +P + V+KKLGE+W+ ++K
Sbjct: 8 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDK 49
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPE--MDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAA 131
+ + ++Y + + R++ K +P+ ++FS+ SKK E W T+ EK ++ A A
Sbjct: 9 RGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 68
Query: 132 KYTQKM 137
+Y ++M
Sbjct: 69 RYEREM 74
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPE--MDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAA 131
+ + ++Y + + R++ K +P+ ++F++ SKK E W T+ EK ++ A A
Sbjct: 10 RGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKA 69
Query: 132 KYTQKM 137
+Y ++M
Sbjct: 70 RYDREM 75
>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 = 32.7 bits (73), Expect = 0.22, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 39/66 (59%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+A+ L+ + R K+ +P + V+KKLGE+W+ ++K ++++A +L KY + +
Sbjct: 12 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI 71
Query: 138 SKAPAQ 143
+ A+
Sbjct: 72 AAYRAK 77
>pdb|2V0H|A Chain A, Characterization Of Substrate Binding And Catalysis Of The
Potential Antibacterial Target N-Acetylglucosamine-1-
Phosphate Uridyltransferase (Glmu)
pdb|2V0I|A Chain A, Characterization Of Substrate Binding And Catalysis Of The
Potential Antibacterial Target N-Acetylglucosamine-1-
Phosphate Uridyltransferase (Glmu)
pdb|2V0J|A Chain A, Characterization Of Substrate Binding And Catalysis Of The
Potential Antibacterial Target N-acetylglucosamine-1-
Phosphate Uridyltransferase (glmu)
pdb|2V0K|A Chain A, Characterization Of Substrate Binding And Catalysis Of The
Potential Antibacterial Target N-Acetylglucosamine-1-
Phosphate Uridyltransferase (Glmu)
pdb|2V0L|A Chain A, Characterization Of Substrate Binding And Catalysis Of The
Potential Antibacterial Target N-Acetylglucosamine-1-
Phosphate Uridyltransferase (Glmu)
pdb|2VD4|A Chain A, Structure Of Small-Molecule Inhibitor Of Glmu From
Haemophilus Influenzae Reveals An Allosteric Binding
Site
pdb|2W0V|A Chain A, Crystal Structure Of Glmu From Haemophilus Influenzae In
Complex With Quinazoline Inhibitor 1
pdb|2W0W|A Chain A, Crystal Structure Of Glmu From Haemophilus Influenzae In
Complex With Quinazoline Inhibitor 2
Length = 456
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 3/92 (3%)
Query: 108 GELWHTVPFNEKYGWKRQADRLAAKYTQKMSKAPAQKTKSTYTPHGRVGRPPLNKQTVEA 167
G+L T NE+ W Q ++L + + + + ++ +G P + K+T+E
Sbjct: 59 GDLMRTHLANEQVNWVLQTEQLGTAHAVQQAAPFFKDNENIVVLYGDA--PLITKETLEK 116
Query: 168 VIETKP-SPPAAPRVPLVKPTLPADLFKVTGT 198
+IE KP + A V L PT + + G
Sbjct: 117 LIEAKPENGIALLTVNLDNPTGYGRIIRENGN 148
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 36/64 (56%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
KA T Y+ + + R+++ +P++ F +++K LG W + EK + +A++ +Y
Sbjct: 9 KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQY 68
Query: 134 TQKM 137
+++
Sbjct: 69 LKEL 72
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 29.3 bits (64), Expect = 2.8, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 28/57 (49%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLA 130
K A+ML+AK+ R + + P D +S LG+ W + E+ + +A LA
Sbjct: 19 KRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALA 75
>pdb|4AG5|A Chain A, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG5|B Chain B, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG5|C Chain C, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
pdb|4AG5|D Chain D, Structure Of Virb4 Of Thermoanaerobacter Pseudethanolicus
Length = 392
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 77 FTAYMLWAKQIRQ--KLIKSNPEMDFSQVSKKLGELW 111
FTA ML ++ Q ++I +PE ++ ++ +KLG +W
Sbjct: 50 FTAKMLLLREYMQGSRVIIIDPEREYKEMCRKLGGVW 86
>pdb|1IOO|A Chain A, Crystal Structure Of Nicotiana Alata Gemetophytic
Self-incompatibility Associated Sf11-rnase
pdb|1IOO|B Chain B, Crystal Structure Of Nicotiana Alata Gemetophytic
Self-incompatibility Associated Sf11-rnase
Length = 196
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 10/66 (15%)
Query: 70 ESIEKARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKK----LGELWHTVPFNEKYG---- 121
E I FT + LW ++ +L P+ +S + K L + W + F + YG
Sbjct: 22 ERIAPNNFTIHGLWPDNVKTRLHNCKPKPTYSYFTGKMLNDLDKHWMQLKFEQDYGRTEQ 81
Query: 122 --WKRQ 125
WK Q
Sbjct: 82 PSWKYQ 87
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 28.5 bits (62), Expect = 4.2, Method: Composition-based stats.
Identities = 11/46 (23%), Positives = 25/46 (54%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEK 119
K A+ML+ K++R ++ + + + +++ LG WH + E+
Sbjct: 4 KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQ 49
>pdb|2CO9|A Chain A, Solution Structure Of The Hmg_box Domain Of Thymus High
Mobility Group Box Protein Tox From Mouse
Length = 102
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 37/76 (48%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+AY L+ + + + NP F +VSK + +W + +K +K++ + +Y +++
Sbjct: 23 SAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQL 82
Query: 138 SKAPAQKTKSTYTPHG 153
+ A +YT G
Sbjct: 83 AAYRASLVSKSYTDSG 98
>pdb|4EA7|A Chain A, X-Ray Crystal Structure Of Perb From Caulobacter
Crescentus In Complex With Coa And Gdp-Perosamine At 1.0
Angstrom Resolution
pdb|4EA8|A Chain A, X-Ray Crystal Structure Of Perb From Caulobacter
Crescentus In Complex With Coenzyme A And
Gdp-N-Acetylperosamine At 1 Angstrom Resolution
pdb|4EA9|A Chain A, X-Ray Structure Of Gdp-Perosamine N-Acetyltransferase In
Complex With Transition State Analog At 0.9 Angstrom
Resolution
Length = 220
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 163 QTVEAVIETKPSPPAAPRVPLVKPTLPADLFKVTGTQPLDIAAHLRLLGDNLTIIGERLK 222
+TV A+++ P+ A VP+V L + + G L +A +GDN RL+
Sbjct: 36 ETVAAIVDADPTRRAVLGVPVVGDDLALPMLREQGLSRLFVA-----IGDN------RLR 84
Query: 223 DTQGRMAISGGMSLL 237
GR A G SL+
Sbjct: 85 QKLGRKARDHGFSLV 99
>pdb|4EAA|A Chain A, X-Ray Crystal Structure Of The H141n Mutant Of Perosamine
N- Acetyltransferase From Caulobacter Crescentus In
Complex With Coa And Gdp-Perosamine
Length = 220
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 163 QTVEAVIETKPSPPAAPRVPLVKPTLPADLFKVTGTQPLDIAAHLRLLGDNLTIIGERLK 222
+TV A+++ P+ A VP+V L + + G L +A +GDN RL+
Sbjct: 36 ETVAAIVDADPTRRAVLGVPVVGDDLALPMLREQGLSRLFVA-----IGDN------RLR 84
Query: 223 DTQGRMAISGGMSLL 237
GR A G SL+
Sbjct: 85 QKLGRKARDHGFSLV 99
>pdb|4EZB|A Chain A, Crystal Structure Of The Conserved Hypothetical Protein
From Sinorhizobium Meliloti 1021
Length = 317
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 10/45 (22%)
Query: 175 PPAAPRVPLVKPTLPADLFKVTGTQPLDIAAHLRLLGDNLTIIGE 219
PP A +VP++ V G + +++A L LG NL +GE
Sbjct: 152 PPYAEKVPIL----------VAGRRAVEVAERLNALGXNLEAVGE 186
>pdb|4EAB|A Chain A, X-Ray Crystal Structure Of The H141a Mutant Of
Gdp-Perosamine N-Acetyl Transferase From Caulobacter
Crescentus In Complex With Coa And Gdp- Perosamine
Length = 220
Score = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 163 QTVEAVIETKPSPPAAPRVPLVKPTLPADLFKVTGTQPLDIAAHLRLLGDNLTIIGERLK 222
+TV A+++ P+ A VP+V L + + G L +A +GDN RL+
Sbjct: 36 ETVAAIVDADPTRRAVLGVPVVGDDLALPMLREQGLSRLFVA-----IGDN------RLR 84
Query: 223 DTQGRMAISGGMSLL 237
GR A G SL+
Sbjct: 85 QKLGRKARDHGFSLV 99
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
0.314 0.132 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,380,549
Number of Sequences: 62578
Number of extensions: 341079
Number of successful extensions: 607
Number of sequences better than 100.0: 53
Number of HSP's better than 100.0 without gapping: 37
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 567
Number of HSP's gapped (non-prelim): 55
length of query: 280
length of database: 14,973,337
effective HSP length: 98
effective length of query: 182
effective length of database: 8,840,693
effective search space: 1609006126
effective search space used: 1609006126
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: 51 (24.3 bits)