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= psy16713
(357 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 88.6 bits (218), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 38/68 (55%), Positives = 50/68 (73%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAH 130
RRPMNAF++F KRHR+ V Q HP DNR +KIL +WW L P+EKQKY ++A E K+A
Sbjct: 9 RRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAF 68
Query: 131 FKAHPEWK 138
KA+P ++
Sbjct: 69 MKANPGYR 76
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 65.1 bits (157), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 49/76 (64%)
Query: 70 IRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEA 129
I+RPMNAFM+++K R K+ Q P+ N +SKILG W ++ EKQ Y+E + + +
Sbjct: 5 IKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQ 64
Query: 130 HFKAHPEWKWCSKDKR 145
H + +P++K+ + KR
Sbjct: 65 HLEKYPDYKYKPRPKR 80
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 64.7 bits (156), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 49/74 (66%), Gaps = 1/74 (1%)
Query: 66 SKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASE 125
S ++ +RPMNAFM+F+K++R + Q++P +DNR +S ILG+ W + EE++ Y A
Sbjct: 14 SPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKA 73
Query: 126 VKEAHFKAHPE-WK 138
+ E + +P+ WK
Sbjct: 74 LAEEQKRLNPDCWK 87
>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 = 62.0 bits (149), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 31/80 (38%), Positives = 49/80 (61%)
Query: 68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVK 127
DR++RPMNAFM++S+ R K+ Q +P N +SK LG W L EK+ + + A ++
Sbjct: 6 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 65
Query: 128 EAHFKAHPEWKWCSKDKRKS 147
H K HP++K+ + K K+
Sbjct: 66 ALHMKEHPDYKYRPRRKTKT 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 = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 31/80 (38%), Positives = 49/80 (61%)
Query: 68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVK 127
DR++RPMNAFM++S+ R K+ Q +P N +SK LG W L EK+ + + A ++
Sbjct: 2 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 61
Query: 128 EAHFKAHPEWKWCSKDKRKS 147
H K HP++K+ + K K+
Sbjct: 62 ALHMKEHPDYKYRPRRKTKT 81
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 61.6 bits (148), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 31/80 (38%), Positives = 49/80 (61%)
Query: 68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVK 127
DR++RPMNAFM++S+ R K+ Q +P N +SK LG W L EK+ + + A ++
Sbjct: 1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 60
Query: 128 EAHFKAHPEWKWCSKDKRKS 147
H K HP++K+ + K K+
Sbjct: 61 ALHMKEHPDYKYRPRRKTKT 80
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 47/71 (66%)
Query: 69 RIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKE 128
RIRRPMNAFM+++K R ++ Q +P+ N +SK+LG+ W +L EK+ + E A ++
Sbjct: 6 RIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 65
Query: 129 AHFKAHPEWKW 139
H + HP +K+
Sbjct: 66 QHMQDHPNYKY 76
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 70 IRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEA 129
IRRPMNAFM+++K R ++ Q +P+ N +SK+LG+ W +L EK+ + E A ++
Sbjct: 8 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 67
Query: 130 HFKAHPEWK 138
H + HP +K
Sbjct: 68 HMQDHPNYK 76
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 45/69 (65%)
Query: 70 IRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEA 129
IRRPMNAFM+++K R ++ Q +P+ N +SK+LG+ W +L EK+ + E A ++
Sbjct: 3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 130 HFKAHPEWK 138
H + HP +K
Sbjct: 63 HMQDHPNYK 71
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 57.8 bits (138), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 45/68 (66%)
Query: 70 IRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEA 129
I++P+NAFM++ K RA V +++ +++ILG W++L EE+ KY+ELA + ++
Sbjct: 3 IKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQL 62
Query: 130 HFKAHPEW 137
H + +P W
Sbjct: 63 HMQLYPGW 70
>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 = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 52/83 (62%), Gaps = 1/83 (1%)
Query: 65 RSKDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELAS 124
++K ++RPMNAFM++++ R K+ +P+ N +SK LG+ W L EK+ + E A
Sbjct: 25 KNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAE 84
Query: 125 EVKEAHFKAHPEWKWCSKDKRKS 147
++ H K HP++K+ + +RKS
Sbjct: 85 RLRVQHKKDHPDYKYQPR-RRKS 106
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 67 KDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEV 126
+DR++RPMNAF+++S+ R K+ +P N +SK LG W L EK + + A ++
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61
Query: 127 KEAHFKAHPEWKW 139
+ H + +P +K+
Sbjct: 62 QAMHREKYPNYKY 74
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKY 119
+RP +AF +F +R K+ HP V+K LGE W + ++KQ Y
Sbjct: 90 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 138
>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 = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 47/80 (58%)
Query: 67 KDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEV 126
+DR++RPMNAF+++S+ R K+ +P N +SK LG W L EK + + A ++
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61
Query: 127 KEAHFKAHPEWKWCSKDKRK 146
+ H + +P +K+ + K K
Sbjct: 62 QAMHREKYPNYKYRPRRKAK 81
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 67 KDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEV 126
+DR++RPMNAF+++S+ R K+ +P N +SK LG W L EK + + A ++
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61
Query: 127 KEAHFKAHPEWKW 139
+ H + +P +K+
Sbjct: 62 QAMHREKYPNYKY 74
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 45/77 (58%)
Query: 70 IRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEA 129
I+RPMNAFM++S+ R K+ + P+ N +SK LG+ W L +K + + A ++
Sbjct: 3 IKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62
Query: 130 HFKAHPEWKWCSKDKRK 146
H +P++K+ + K K
Sbjct: 63 HMADYPDYKYRPRKKVK 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 = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 47/80 (58%)
Query: 67 KDRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEV 126
+DR++RP+NAF+++S+ R K+ +P N +SK LG W L EK + + A ++
Sbjct: 2 QDRVKRPINAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61
Query: 127 KEAHFKAHPEWKWCSKDKRK 146
+ H + +P +K+ + K K
Sbjct: 62 QAMHREKYPNYKYRPRRKAK 81
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 36/68 (52%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAH 130
+RP + F +F R K+ +P V+K LGE W +L EKQ Y A+++KE +
Sbjct: 11 KRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKY 70
Query: 131 FKAHPEWK 138
K ++K
Sbjct: 71 EKDVADYK 78
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 33/60 (55%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAH 130
+RP +AF +F HR K+ HP +K LGE W ++KQ Y + A+++KE +
Sbjct: 9 KRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKY 68
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 33/60 (55%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAH 130
+RP +AF +F +R K+ HP +K LGE W ++KQ Y + A+++KE +
Sbjct: 10 KRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKY 69
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 2/80 (2%)
Query: 73 PMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAHFK 132
P+ ++ F R ++ HP+ ++K+LG W L P EKQ+Y + A + K+ + K
Sbjct: 11 PVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLK 70
Query: 133 AHPEWKWCSKDKRKSSTGSG 152
W + + K T SG
Sbjct: 71 EL--WAYQQSEAYKVCTESG 88
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 29/50 (58%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYH 120
+R ++A+M F+ +R V +P+ V K LGE W +L PEEKQ Y
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYE 71
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 29/50 (58%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYH 120
+R ++A+M F+ +R V +P+ V K LGE W +L PEEKQ Y
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYE 71
>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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKY 119
+RP +AF +F +R K+ HP V+K LGE W + ++KQ Y
Sbjct: 6 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 54
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 41/84 (48%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVKEAH 130
++P++A+ +F + +A + +PN VSKI+ W LG E+KQ Y + K+ +
Sbjct: 19 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEY 78
Query: 131 FKAHPEWKWCSKDKRKSSTGSGRG 154
K ++ K + +G G
Sbjct: 79 LKQLAAYRASLVSKSYTDSGPSSG 102
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKY 119
+RP +AF +F +R K+ HP V+K LGE W + ++KQ Y
Sbjct: 8 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 56
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKY 119
+RP +AF +F +R K+ HP V+K LGE W + ++KQ Y
Sbjct: 103 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 151
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVK 127
++ +RP++A IFS+ R ++ + P ++++L W L ++K KY +
Sbjct: 19 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYK-----AR 73
Query: 128 EAHFKAHPEWK 138
EA KA E K
Sbjct: 74 EAALKAQSERK 84
>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 = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 71 RRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKY 119
+RP +AF +F +R K+ HP V+K LGE W + ++KQ Y
Sbjct: 4 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 52
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKY 119
D ++P+ + F RAK ++HP N ++KIL + + L ++K KY
Sbjct: 9 DFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKY 60
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVK 127
D+ +RP++A+M++ R + + +P V+K GE W ++ ++K ++ A++ K
Sbjct: 3 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 60
Query: 128 EAHFKAHPEWK 138
+ + +A E++
Sbjct: 61 DDYDRAVKEFE 71
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVK 127
D+ +RP++A+M++ R + + +P V+K GE W ++ ++K ++ A++ K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 128 EAHFKAHPEWK 138
+ + +A E++
Sbjct: 60 DDYDRAVKEFE 70
>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 = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 41/71 (57%), Gaps = 2/71 (2%)
Query: 68 DRIRRPMNAFMIFSKRHRAKVHQIHPNQDNRTVSKILGEWWYSLGPEEKQKYHELASEVK 127
D+ +RP++A+M++ R + + +P V+K GE W ++ ++K ++ A++ K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 128 EAHFKAHPEWK 138
+ + +A E++
Sbjct: 60 DDYDRAVKEFE 70
>pdb|2PTR|A Chain A, Crystal Structure Of Escherichia Coli Adenylosuccinate
Lyase Mutant H171a With Bound Adenylosuccinate Substrate
pdb|2PTR|B Chain B, Crystal Structure Of Escherichia Coli Adenylosuccinate
Lyase Mutant H171a With Bound Adenylosuccinate Substrate
Length = 462
Score = 27.7 bits (60), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 170 DDLEHFENSLEMVTSSNETTVQYLLHPTGRLSNIYSTGFQIPISSESLGNVKQPTTPTVI 229
+D+ + ++L + T+ +E + Y L ++ IP+ S + G QP TP+ I
Sbjct: 124 EDINNLSHALMLKTARDEVILPYWRQLIDGLKDLAVQYRDIPLLSRTAG---QPATPSTI 180
Query: 230 VSKQSNI 236
+ +N+
Sbjct: 181 GKEMANV 187
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
0.311 0.127 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,655,124
Number of Sequences: 62578
Number of extensions: 433060
Number of successful extensions: 734
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 702
Number of HSP's gapped (non-prelim): 41
length of query: 357
length of database: 14,973,337
effective HSP length: 100
effective length of query: 257
effective length of database: 8,715,537
effective search space: 2239893009
effective search space used: 2239893009
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)