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= psy1729
(170 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 = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/45 (53%), Positives = 35/45 (77%)
Query: 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY 95
++TK+LG EWSKL EK+ YLD AE +K++Y +EL Y++S+AY
Sbjct: 37 EITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAY 81
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/35 (57%), Positives = 27/35 (77%)
Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 50
+TK+LG EWSKL EK+ YLD AE +K++Y +EL
Sbjct: 38 ITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKEL 72
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 34.7 bits (78), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
+V K LG +W L+ EK+ Y +A+ DKKRY E ++Y
Sbjct: 50 QVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY 88
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 49
V K LG +W L+ EK+ Y +A+ DKKRY E
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
>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 = 34.7 bits (78), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
+V K LG +W L+ EK+ Y +A+ DKKRY E ++Y
Sbjct: 50 QVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELY 88
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 21/34 (61%)
Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 49
V K LG +W L+ EK+ Y +A+ DKKRY E
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 29.6 bits (65), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
+K W +S EK + D A+ DK RY E+K Y
Sbjct: 34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71
Score = 27.3 bits (59), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV 52
+K W +S EK + D A+ DK RY E+K
Sbjct: 34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKT 70
>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 = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
+K W +S EK + D A+ DK RY E+K Y
Sbjct: 40 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 77
Score = 26.6 bits (57), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV 52
+K W +S EK + D A+ DK RY E+K
Sbjct: 40 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKT 76
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 60 WSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
W +S EK + D A+ DK RY E+K Y
Sbjct: 48 WKTMSAKEKGKFEDMAKADKARYEREMKTY 77
Score = 26.6 bits (57), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 24 WSKLSLPEKKVYLDRAEVDKKRYREELKV 52
W +S EK + D A+ DK RY E+K
Sbjct: 48 WKTMSAKEKGKFEDMAKADKARYEREMKT 76
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From
Human High Mobility Group Protein B1
Length = 173
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 60 WSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
W +S EK + D A+ DK RY E+K Y
Sbjct: 56 WKTMSAKEKGKFEDMAKADKARYEREMKTY 85
>pdb|4DGW|A Chain A, Crystal Structure Of The Sf3a Splicing Factor Complex Of
U2 Snrnp
Length = 402
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 135 LYCRVCDQWFTTLHNKREHLNGRQH 159
+YC C +WF T HL G+ H
Sbjct: 293 IYCPFCSRWFKTSSVFESHLVGKIH 317
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAE 40
++K+LG W L+L EK+ +++ AE
Sbjct: 37 LSKMLGKSWKALTLAEKRPFVEEAE 61
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAE 76
++K+LG W L+L EK+ +++ AE
Sbjct: 37 LSKMLGKSWKALTLAEKRPFVEEAE 61
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAE 40
++K+LG W L+L EK+ +++ AE
Sbjct: 33 LSKMLGKSWKALTLAEKRPFVEEAE 57
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAE 76
++K+LG W L+L EK+ +++ AE
Sbjct: 33 LSKMLGKSWKALTLAEKRPFVEEAE 57
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAE 40
++K+LG W L+L EK+ +++ AE
Sbjct: 38 LSKMLGKSWKALTLAEKRPFVEEAE 62
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAE 76
++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 = 27.3 bits (59), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 54 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
K + W LS EK++Y+ A+ D+ RY E+K +
Sbjct: 31 KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW 66
Score = 26.9 bits (58), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 18 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
K + W LS EK++Y+ A+ D+ RY E+K
Sbjct: 31 KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMK 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 = 26.9 bits (58), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 9 ISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 49
I+ + K++G W+ LS EKK Y ++ D+ RY E
Sbjct: 48 IAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYERE 88
Score = 26.6 bits (57), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
+ K++G W+ LS EKK Y ++ D+ RY E Y
Sbjct: 55 IGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEY 92
>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 = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 54 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS--DAYQSYLRRKRVKSLQANG 111
K + W LS EK++Y+ A+ D+ RY E+K + + + + L R+ +K + G
Sbjct: 143 KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKKQRKYG 202
Query: 112 TEE 114
EE
Sbjct: 203 AEE 205
Score = 26.2 bits (56), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 18 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
K + W LS EK++Y+ A+ D+ RY E+K
Sbjct: 143 KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMK 176
>pdb|2ZXH|A Chain A, Structure Of Aquifex Aeolicus Gida In The Form I Crystal
pdb|2ZXH|B Chain B, Structure Of Aquifex Aeolicus Gida In The Form I Crystal
pdb|2ZXI|A Chain A, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
pdb|2ZXI|B Chain B, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
pdb|2ZXI|C Chain C, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
pdb|2ZXI|D Chain D, Structure Of Aquifex Aeolicus Gida In The Form Ii Crystal
Length = 637
Score = 26.9 bits (58), Expect = 6.0, Method: Composition-based stats.
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 32 KKVYLDRAEVDKKRYREELK 51
K V RA+ DKKRYRE +K
Sbjct: 111 KAVQSPRAQADKKRYREYMK 130
Score = 26.9 bits (58), Expect = 6.0, Method: Composition-based stats.
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 68 KKVYLDRAEVDKKRYREELK 87
K V RA+ DKKRYRE +K
Sbjct: 111 KAVQSPRAQADKKRYREYMK 130
>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 = 26.6 bits (57), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY 98
+V+K++ + W L +K+VY + E KK Y ++L YR S +SY
Sbjct: 47 EVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSY 94
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From
High Mobility Group Protein B3
Length = 81
Score = 26.2 bits (56), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 24/39 (61%)
Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90
V K LG W+ L+ EK+ Y+ +A K++Y +++ Y+
Sbjct: 40 VAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADYK 78
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 26.2 bits (56), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 1 MDIESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRA 39
M E+ KM ++ ++K LG EW LS EK+ ++D A
Sbjct: 22 MAQENPKMHNSE---ISKRLGAEWKLLSETEKRPFIDEA 57
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 26.2 bits (56), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 1 MDIESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRA 39
M E+ KM ++ ++K LG EW LS EK+ ++D A
Sbjct: 21 MAQENPKMHNSE---ISKRLGAEWKLLSETEKRPFIDEA 56
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 0.132 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,491,010
Number of Sequences: 62578
Number of extensions: 153603
Number of successful extensions: 614
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 37
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 539
Number of HSP's gapped (non-prelim): 83
length of query: 170
length of database: 14,973,337
effective HSP length: 92
effective length of query: 78
effective length of database: 9,216,161
effective search space: 718860558
effective search space used: 718860558
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)