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= psy6088
(289 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 191 bits (485), Expect = 4e-49, Method: Compositional matrix adjust.
Identities = 96/129 (74%), Positives = 111/129 (86%), Gaps = 3/129 (2%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLL+KW
Sbjct: 7 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKW 66
Query: 218 LSDADSTTANPSCLSNPLTTP---EAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEI 274
L+DA++ +++ S S E + RRRKKRTSIET++RVALEK+FL+N KPTSEEI
Sbjct: 67 LNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEI 126
Query: 275 SVLADNLCM 283
+++AD L M
Sbjct: 127 TMIADQLNM 135
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 191 bits (484), Expect = 5e-49, Method: Compositional matrix adjust.
Identities = 96/129 (74%), Positives = 111/129 (86%), Gaps = 3/129 (2%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLL+KW
Sbjct: 14 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKW 73
Query: 218 LSDADSTTANPSCLSNPLTTP---EAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEI 274
L+DA++ +++ S S E + RRRKKRTSIET++RVALEK+FL+N KPTSEEI
Sbjct: 74 LNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEI 133
Query: 275 SVLADNLCM 283
+++AD L M
Sbjct: 134 TMIADQLNM 142
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 189 bits (481), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 95/129 (73%), Positives = 110/129 (85%), Gaps = 3/129 (2%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNM KLKPLL+KW
Sbjct: 11 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPLLEKW 70
Query: 218 LSDADSTTANPSCLSNPLTTP---EAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEI 274
L+DA++ +++ S S E + RRRKKRTSIET++RVALEK+FL+N KPTSEEI
Sbjct: 71 LNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEI 130
Query: 275 SVLADNLCM 283
+++AD L M
Sbjct: 131 TMIADQLNM 139
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 186 bits (471), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 94/129 (72%), Positives = 109/129 (84%), Gaps = 3/129 (2%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNM KLKPLL+KW
Sbjct: 15 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMAKLKPLLEKW 74
Query: 218 LSDADSTTANPSCLSNPLTTP---EAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEI 274
L+DA++ +++ S S E + RRKKRTSIET++RVALEK+FL+N KPTSEEI
Sbjct: 75 LNDAENLSSDSSLSSPSALNSPGIEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEI 134
Query: 275 SVLADNLCM 283
+++AD L M
Sbjct: 135 TMIADQLNM 143
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 186 bits (471), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 94/130 (72%), Positives = 112/130 (86%), Gaps = 4/130 (3%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNM KLKPLL+KW
Sbjct: 11 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMSKLKPLLEKW 70
Query: 218 LSDADSTTANPSCLSNPLTTP----EAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSEE 273
L+DA++ ++ S LS+P E + RRRKKRTSIET++RVALEK+F++N KPTSE+
Sbjct: 71 LNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSED 130
Query: 274 ISVLADNLCM 283
I+++A+ L M
Sbjct: 131 ITLIAEQLNM 140
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 164 bits (416), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 83/124 (66%), Positives = 96/124 (77%), Gaps = 4/124 (3%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFAK FKQRRIKLGFTQ DVGLA+G LYGN FSQTTI RFEAL LSFKNMCKLKPLL KW
Sbjct: 17 QFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLNKW 76
Query: 218 LSDADSTTANPSCLSNPLTTPEAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVL 277
L + DS++ +P+ L A GR+RKKRTSIE V+ ALE FL+ PKP++ EI+ L
Sbjct: 77 LEETDSSSGSPT----NLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGL 132
Query: 278 ADNL 281
AD+L
Sbjct: 133 ADSL 136
>pdb|1POU|A Chain A, The Solution Structure Of The Oct-1 Pou-Specific Domain
Reveals A Striking Similarity To The Bacteriophage
Lambda Repressor Dna-Binding Domain
Length = 71
Score = 135 bits (339), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 62/65 (95%), Positives = 65/65 (100%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLL+KW
Sbjct: 7 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKW 66
Query: 218 LSDAD 222
L+DA+
Sbjct: 67 LNDAE 71
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 133 bits (335), Expect = 9e-32, Method: Compositional matrix adjust.
Identities = 68/126 (53%), Positives = 91/126 (72%), Gaps = 4/126 (3%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFAK KQ+RI LG+TQ DVGL +G L+G FSQTTISRFEAL LS KNM KL+PLL+KW
Sbjct: 14 QFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQLSLKNMSKLRPLLEKW 73
Query: 218 LSDADSTTANPSCLSNPLTTPEAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVL 277
+ +AD+ N +S T +A R++KRTSIE VR +LE FL++PKP+ ++I+ +
Sbjct: 74 VEEADN-NENLQEISKSETLVQA---RKRKRTSIENRVRWSLETMFLKSPKPSLQQITHI 129
Query: 278 ADNLCM 283
A+ L +
Sbjct: 130 ANQLGL 135
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 119 bits (298), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 63/127 (49%), Positives = 86/127 (67%), Gaps = 12/127 (9%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
QFA FK RRIKLG+TQ +VG A+ ++G++FSQTTI RFE L LSFKN CKLK +L KW
Sbjct: 7 QFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKW 66
Query: 218 LSDADSTTANPSCLSNPLTTPEAIG---RRRKKRTSIETSVRVALEKAFLQNPKPTSEEI 274
L +A+ A L N E +G R+RK+RT+I + + ALE+ F ++ KP+S+EI
Sbjct: 67 LEEAEQVGA----LYN-----EKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEI 117
Query: 275 SVLADNL 281
+A+ L
Sbjct: 118 MRMAEEL 124
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 82.4 bits (202), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 53/131 (40%), Positives = 74/131 (56%), Gaps = 9/131 (6%)
Query: 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217
+FAK FK RR+ LG TQ VG A G +SQ+ ISRFE L+++ K+ KLKP+L+KW
Sbjct: 8 EFAKNFKIRRLSLGLTQTQVGQAXTATEGPAYSQSAISRFEKLDITPKSAQKLKPVLEKW 67
Query: 218 LSDADSTTANPSCLSNPLTTPEAIG----RRRKKRTSIETSVRVALEKAFLQNPKPTSEE 273
L++A+ N N E +G ++RK+RTS AL F +NP PT +E
Sbjct: 68 LNEAE--LRNQEGQQN---LXEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQE 122
Query: 274 ISVLADNLCMN 284
I+ A L +
Sbjct: 123 ITEXAKELNYD 133
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 64.3 bits (155), Expect = 6e-11, Method: Composition-based stats.
Identities = 31/41 (75%), Positives = 38/41 (92%)
Query: 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCM 283
RRRKKRTSIET++RVALEK+FL+N KPTSEEI+++AD L M
Sbjct: 6 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNM 46
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 57.8 bits (138), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 29/40 (72%), Positives = 34/40 (85%)
Query: 244 RRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCM 283
RRKKRTSIET+VR ALEK+FL N KPTSEEI ++A+ L M
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHM 40
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 29/38 (76%)
Query: 244 RRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNL 281
R++KRTSIE VR +LE FL+ PKP+ ++I+ +A+ L
Sbjct: 8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQL 45
>pdb|2P22|D Chain D, Structure Of The Yeast Escrt-i Heterotetramer Core
Length = 79
Score = 30.8 bits (68), Expect = 0.98, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 185 YGNDFSQTTISRFEALNLSFKNMCKLKPLLQKWLSDADSTT 225
YG DF Q T++RF+ + + LL W + D+ T
Sbjct: 16 YGKDFPQETVTRFQMPEFKLPALQPTRDLLCPWYEECDNIT 56
>pdb|1GPM|A Chain A, Escherichia Coli Gmp Synthetase Complexed With Amp And
Pyrophosphate
pdb|1GPM|B Chain B, Escherichia Coli Gmp Synthetase Complexed With Amp And
Pyrophosphate
pdb|1GPM|C Chain C, Escherichia Coli Gmp Synthetase Complexed With Amp And
Pyrophosphate
pdb|1GPM|D Chain D, Escherichia Coli Gmp Synthetase Complexed With Amp And
Pyrophosphate
Length = 525
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 211 KPLLQKWLSDADSTTANPSCLSNPLTT---PEAIGRRRKKR 248
KPLL W+S D TA PS +T P AI +KR
Sbjct: 134 KPLLDVWMSHGDKVTAIPSDFITVASTESCPFAIMANEEKR 174
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 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,964,788
Number of Sequences: 62578
Number of extensions: 139812
Number of successful extensions: 313
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 290
Number of HSP's gapped (non-prelim): 15
length of query: 289
length of database: 14,973,337
effective HSP length: 98
effective length of query: 191
effective length of database: 8,840,693
effective search space: 1688572363
effective search space used: 1688572363
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: 51 (24.3 bits)