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= psy1990
(382 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 38/50 (76%)
Query: 50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 99
L F ++TK+LG EWSKL EK+ YLD AE +K++Y +EL Y++S+AY+
Sbjct: 33 LPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYK 82
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/45 (53%), Positives = 35/45 (77%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 45
+TK+LG EWSKL EK+ YLD AE +K++Y +EL Y++S+AY+
Sbjct: 38 ITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYK 82
>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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 27/43 (62%)
Query: 50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
+ F QV K LG +W L+ EK+ Y +A+ DKKRY E ++Y
Sbjct: 46 ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY 88
Score = 35.0 bits (79), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 24/38 (63%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
V K LG +W L+ EK+ Y +A+ DKKRY E ++Y
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY 88
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 27/43 (62%)
Query: 50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
+ F QV K LG +W L+ EK+ Y +A+ DKKRY E ++Y
Sbjct: 46 ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY 88
Score = 35.0 bits (79), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 24/38 (63%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
V K LG +W L+ EK+ Y +A+ DKKRY E ++Y
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY 88
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
F + +K W +S EK + D A+ DK RY E+K Y
Sbjct: 31 FSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
+K W +S EK + D A+ DK RY E+K Y
Sbjct: 34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 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 = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
F + +K W +S EK + D A+ DK RY E+K Y
Sbjct: 37 FSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 77
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
+K W +S EK + D A+ DK RY E+K Y
Sbjct: 40 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 77
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 32.3 bits (72), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
F + +K W +S EK + D A+ DK RY E+K Y
Sbjct: 37 FSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 77
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
+K W +S EK + D A+ DK RY E+K Y
Sbjct: 40 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 77
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From
Human High Mobility Group Protein B1
Length = 173
Score = 32.0 bits (71), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
F + +K W +S EK + D A+ DK RY E+K Y
Sbjct: 45 FSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 85
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 29/123 (23%), Positives = 46/123 (37%), Gaps = 30/123 (24%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY------------------RKSD 42
+K W +S EK + D A+ DK RY E+K Y R
Sbjct: 48 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPS 107
Query: 43 AY------------QSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
A+ + L V K LG W+ + +K+ Y +A K++Y +++
Sbjct: 108 AFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA 167
Query: 91 VYR 93
YR
Sbjct: 168 AYR 170
>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 = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY 101
F +V+K++ + W L +K+VY + E KK Y ++L YR S +SY
Sbjct: 45 FGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSY 94
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
F + +K W +S EK + D A+ DK RY E+K
Sbjct: 38 FAEFSKKCSERWKTMSAKEKSKFEDMAKSDKARYDREMK 76
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAE 79
+++K+LG W L+L EK+ +++ AE
Sbjct: 36 ELSKMLGKSWKALTLAEKRPFVEEAE 61
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAE 25
++K+LG W L+L EK+ +++ AE
Sbjct: 37 LSKMLGKSWKALTLAEKRPFVEEAE 61
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 28.5 bits (62), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAE 79
+++K+LG W L+L EK+ +++ AE
Sbjct: 37 ELSKMLGKSWKALTLAEKRPFVEEAE 62
Score = 27.7 bits (60), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAE 25
++K+LG W L+L EK+ +++ AE
Sbjct: 38 LSKMLGKSWKALTLAEKRPFVEEAE 62
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 39 RKSDAYQSYLILLFFQVT--------KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
R AY Y+ F + K + W LS EK++Y+ A+ D+ RY E+K
Sbjct: 5 RPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMK 64
Query: 91 VY 92
+
Sbjct: 65 SW 66
Score = 28.1 bits (61), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 3 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
K + W LS EK++Y+ A+ D+ RY E+K +
Sbjct: 31 KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW 66
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 28.1 bits (61), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAE 79
+++K+LG W L+L EK+ +++ AE
Sbjct: 32 ELSKMLGKSWKALTLAEKRPFVEEAE 57
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From
High Mobility Group Protein B3
Length = 81
Score = 28.1 bits (61), Expect = 8.5, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 24/39 (61%)
Query: 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39
V K LG W+ L+ EK+ Y+ +A K++Y +++ Y+
Sbjct: 40 VAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADYK 78
Score = 28.1 bits (61), Expect = 8.5, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 24/39 (61%)
Query: 55 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93
V K LG W+ L+ EK+ Y+ +A K++Y +++ Y+
Sbjct: 40 VAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADYK 78
>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
Length = 1232
Score = 28.1 bits (61), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 31 YREELKVYRKSDAYQSYLILLFFQV---TKLLGNEWSK------LSLPEKKVYLDRAEVD 81
Y +EL + DA I+ FF +L+G +W L+LP K++Y D E D
Sbjct: 1090 YEKELLTEEQKDAIDIEEIVQFFHTEIGGQLIGAKWKDREIPFSLALPAKEIYPDAHEAD 1149
Query: 82 K 82
+
Sbjct: 1150 E 1150
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
F + +K W +S EK + + A+ DK RY E+K Y
Sbjct: 45 FAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY 85
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
0.315 0.129 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,851,235
Number of Sequences: 62578
Number of extensions: 348453
Number of successful extensions: 980
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 910
Number of HSP's gapped (non-prelim): 74
length of query: 382
length of database: 14,973,337
effective HSP length: 101
effective length of query: 281
effective length of database: 8,652,959
effective search space: 2431481479
effective search space used: 2431481479
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: 52 (24.6 bits)