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= psy1937
(307 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQE 144
P+KP+ Y+R+S++ KAQN D K E+ + I Q WR+LP+ +K Y + Y E
Sbjct: 42 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAE 98
>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
Factor A, Tfam Or Mttfa, Bound To The Light Strand
Promoter Lsp
pdb|3TQ6|B Chain B, Crystal Structure Of Human Mitochondrial Transcription
Factor A, Tfam Or Mttfa, Bound To The Light Strand
Promoter Lsp
Length = 214
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQE 144
P+KP+ Y+R+S++ KAQN D K E+ + I Q WR+LP+ +K Y + Y E
Sbjct: 10 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAE 66
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 85 PKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 137
P P+KP+ Y + R +K QN + E+ KI+ MW L E+QK Y
Sbjct: 15 PNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVY 67
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 40/63 (63%)
Query: 83 KAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYE 142
K P P+KPL PY R+ + + + ++ ++ KI+ + +++LPE +K +Y++D++
Sbjct: 6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQ 65
Query: 143 QEK 145
+EK
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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 85 PKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVED---- 140
P P++ L YM ++ + D V+++N D+ ++GK +G+ W+ L ++K Y
Sbjct: 18 PNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD 77
Query: 141 ---YEQEKNLKAST 151
YE EK L +T
Sbjct: 78 KKRYESEKELYNAT 91
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 85 PKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVED---- 140
P P++ L YM ++ + D V+++N D+ ++GK +G+ W+ L ++K Y
Sbjct: 18 PNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD 77
Query: 141 ---YEQEKNLKAST 151
YE EK L +T
Sbjct: 78 KKRYESEKELYNAT 91
>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 = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 83 KAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLK--LWEIGKIIGQMWRDLPEDQKTEY 137
K P P++ L YM ++++ ++ A+N ++ + IGK+IG W L +++K Y
Sbjct: 18 KDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPY 74
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 28/55 (50%)
Query: 83 KAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 137
K P P++P + + + ++K ++ L + ++ K +G+MW + D K Y
Sbjct: 97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 151
>pdb|3ELQ|A Chain A, Crystal Structure Of A Bacterial Arylsulfate
Sulfotransferase
pdb|3ELQ|B Chain B, Crystal Structure Of A Bacterial Arylsulfate
Sulfotransferase
Length = 571
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 32/123 (26%), Positives = 50/123 (40%), Gaps = 11/123 (8%)
Query: 39 TTNRMQVLKRQVQSLTMHQHCQRVSRRGNVSQKMLTAKTDGRGPKAPKPPEKPLMPYMRY 98
T N + + T QH +S +G LT +G G + E+P +P M+Y
Sbjct: 417 TCNENGLCENSDFDFTYTQHTAWISSKGT-----LTIFDNGDG----RHLEQPALPTMKY 467
Query: 99 SRKVWDQVKAQNLDL-KLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKNLKASTKLASIS 157
SR V ++ + + ++WE GK G + P EY D S L +
Sbjct: 468 SRFVEYKIDEKKGTVQQVWEYGKERGYDFYS-PITSIIEYQADRNTMFGFGGSIHLFDVG 526
Query: 158 RPT 160
+PT
Sbjct: 527 QPT 529
>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 = 32.0 bits (71), Expect = 0.49, Method: Composition-based stats.
Identities = 13/55 (23%), Positives = 28/55 (50%)
Query: 83 KAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 137
K P P++P + + + ++K ++ L + ++ K +G+MW + D K Y
Sbjct: 2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 56
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 32/54 (59%)
Query: 90 KPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQ 143
+P+ +M +++ ++ QN DL E+ K++G+ W+ L +K +VE+ E+
Sbjct: 10 RPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAER 63
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 31.2 bits (69), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 32/54 (59%)
Query: 90 KPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQ 143
+P+ +M +++ ++ QN DL E+ K++G+ W+ L +K +VE+ E+
Sbjct: 9 RPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAER 62
>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 = 30.8 bits (68), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDL 129
P++PL YM + + +K +N +K+ E+ K G++WR +
Sbjct: 4 PKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM 45
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 32/54 (59%)
Query: 90 KPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQ 143
+P+ +M +++ ++ QN DL E+ K++G+ W+ L +K +VE+ E+
Sbjct: 5 RPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAER 58
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDL 129
P++PL YM + + +K +N +K+ E+ K G++WR +
Sbjct: 5 PKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM 46
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDL 129
P++PL YM + + +K +N +K+ E+ K G++WR +
Sbjct: 4 PKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM 45
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 15/73 (20%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 79 GRGPKAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYV 138
G + P++P + + + ++K+ N + + ++ K +G+MW +L + +K Y+
Sbjct: 1 GSSGSSGNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYI 60
Query: 139 -------EDYEQE 144
E YE++
Sbjct: 61 TKAAKLKEKYEKD 73
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 28/55 (50%)
Query: 83 KAPKPPEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 137
K P P++P + + + ++K ++ L + ++ K +G+MW + D K Y
Sbjct: 84 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 138
>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 = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 32/55 (58%)
Query: 89 EKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQ 143
++P+ +M +++ ++ Q L E+ K +G++WR L E +K +VE+ E+
Sbjct: 31 KRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAER 85
>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 = 28.9 bits (63), Expect = 4.0, Method: Composition-based stats.
Identities = 11/50 (22%), Positives = 26/50 (52%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 137
P++P + + + ++K ++ L + ++ K +G+MW + D K Y
Sbjct: 5 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 54
>pdb|1I7O|A Chain A, Crystal Structure Of Hpce
pdb|1I7O|B Chain B, Crystal Structure Of Hpce
pdb|1I7O|C Chain C, Crystal Structure Of Hpce
pdb|1I7O|D Chain D, Crystal Structure Of Hpce
pdb|1GTT|A Chain A, Crystal Structure Of Hpce
pdb|1GTT|B Chain B, Crystal Structure Of Hpce
pdb|1GTT|C Chain C, Crystal Structure Of Hpce
pdb|1GTT|D Chain D, Crystal Structure Of Hpce
Length = 429
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 7/87 (8%)
Query: 86 KPPEKPLMPYMRYSRKVWD----QVKAQNLDLKLWE--IGKIIGQMWRDLPEDQKTEYVE 139
KPPE+PL+ +++ + V+ N++ +E + +IG+ R++ E +YV
Sbjct: 242 KPPEEPLV-FLKAPNTLTGDNQTSVRPNNIEYMHYEAELVVVIGKQARNVSEADAMDYVA 300
Query: 140 DYEQEKNLKASTKLASISRPTWRAKAK 166
Y + L + RP R K++
Sbjct: 301 GYTVCNDYAIRDYLENYYRPNLRVKSR 327
>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 = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 24/42 (57%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDL 129
P++PL Y + + +K +N +K+ E+ K G++WR +
Sbjct: 4 PKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAM 45
>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 = 28.5 bits (62), Expect = 4.9, Method: Composition-based stats.
Identities = 11/50 (22%), Positives = 26/50 (52%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 137
P++P + + + ++K ++ L + ++ K +G+MW + D K Y
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 52
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 88 PEKPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTE 136
P++ +M + + +K +N +K+ EI K G+MW++L + K E
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSKWE 52
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 27.7 bits (60), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 90 KPLMPYMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKNLKA 149
KPL +M Y +++ V A++ + I +I+G+ W L +++ +Y E +E+ L
Sbjct: 5 KPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHM 64
Query: 150 STKLASISRPTWRAK 164
P W A+
Sbjct: 65 QLY------PGWSAR 73
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 0.128 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,899,234
Number of Sequences: 62578
Number of extensions: 282338
Number of successful extensions: 628
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 577
Number of HSP's gapped (non-prelim): 66
length of query: 307
length of database: 14,973,337
effective HSP length: 99
effective length of query: 208
effective length of database: 8,778,115
effective search space: 1825847920
effective search space used: 1825847920
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)