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= psy5907
(56 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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQE-KIYK 56
Y+R+S++ KAQN D K E+ + I Q WR+LP+ +K Y + Y E ++YK
Sbjct: 49 YLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYK 103
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQE-KIYK 56
Y+R+S++ KAQN D K E+ + I Q WR+LP+ +K Y + Y E ++YK
Sbjct: 17 YLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYK 71
>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 = 33.9 bits (76), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 21/43 (48%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 45
Y + R +K QN + E+ KI+ MW L E+QK Y
Sbjct: 25 YALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVY 67
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 27/43 (62%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 45
YM ++ + D V+++N D+ ++GK +G+ W+ L ++K Y
Sbjct: 28 YMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPY 70
>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 = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 27/43 (62%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 45
YM ++ + D V+++N D+ ++GK +G+ W+ L ++K Y
Sbjct: 28 YMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPY 70
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human
Upstream Binding Factor
Length = 99
Score = 32.7 bits (73), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 10/57 (17%)
Query: 2 PYMRY---SRKVWDQVKAQ--NLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEK 53
PY R+ R + ++ + NLDL KI+ + +++LPE +K +Y++D+++EK
Sbjct: 17 PYFRFFMEKRAKYAKLHPEMSNLDL-----TKILSKKYKELPEKKKMKYIQDFQREK 68
>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 = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 10 VWDQVKAQNL-----DLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKI 54
VW Q + L L E+ K +G++WR L E +K +VE+ E+ ++
Sbjct: 39 VWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRV 88
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 17 QNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKI 54
QN DL E+ K++G+ W+ L +K +VE+ E+ ++
Sbjct: 28 QNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 65
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 17 QNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKI 54
QN DL E+ K++G+ W+ L +K +VE+ E+ ++
Sbjct: 29 QNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 66
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 31/52 (59%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYVEDYEQEKI 54
+M +++ ++ QN DL E+ K++G+ W+ L +K +VE+ E+ ++
Sbjct: 10 FMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 61
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From
High Mobility Group Protein B3
Length = 81
Score = 30.0 bits (66), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 9/44 (20%), Positives = 25/44 (56%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEYV 46
+ + + ++K+ N + + ++ K +G+MW +L + +K Y+
Sbjct: 17 FFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYI 60
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 13 QVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 45
++K ++ L + ++ K +G+MW + D K Y
Sbjct: 22 KIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 54
>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 = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/43 (20%), Positives = 22/43 (51%)
Query: 3 YMRYSRKVWDQVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 45
+ + + ++K ++ L + ++ K +G+MW + D K Y
Sbjct: 14 FFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 56
>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 = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 13 QVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 45
++K ++ L + ++ K +G+MW + D K Y
Sbjct: 20 KIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 52
>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 = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 3 YMRYSRKVWDQVKAQNLDLK--LWEIGKIIGQMWRDLPEDQKTEY 45
YM ++++ ++ A+N ++ + IGK+IG W L +++K Y
Sbjct: 30 YMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPY 74
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 12 DQVKAQNLDLKLWEIGKIIGQMWRDLPEDQK 42
+ +K +N +K+ EI K G+MW++L + K
Sbjct: 20 ESIKRENPGIKVTEIAKKGGEMWKELKDKSK 50
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 13 QVKAQNLDLKLWEIGKIIGQMWRDLPEDQKTEY 45
++K ++ L + ++ K +G+MW + D K Y
Sbjct: 106 KIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 138
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
0.317 0.136 0.428
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,933,398
Number of Sequences: 62578
Number of extensions: 58620
Number of successful extensions: 174
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 149
Number of HSP's gapped (non-prelim): 26
length of query: 56
length of database: 14,973,337
effective HSP length: 28
effective length of query: 28
effective length of database: 13,221,153
effective search space: 370192284
effective search space used: 370192284
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)