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= psy17899
(145 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 79.0 bits (193), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 48/121 (39%), Positives = 64/121 (52%), Gaps = 6/121 (4%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIXXXXXXXXXXXXKN 76
G TQADVG AL L SQ+TICRFE+L LS NM LKP+ +
Sbjct: 30 GFTQADVGLALGTLY---GNVFSQTTICRFEALQLSFKNMCKLKPLLNKWLEETDSSSGS 86
Query: 77 KRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVV 136
+ + G K++KRTSI K +LE++F P+PS +I +A+ L L+K VV
Sbjct: 87 P---TNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVV 143
Query: 137 R 137
R
Sbjct: 144 R 144
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 69.3 bits (168), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 49/129 (37%), Positives = 68/129 (52%), Gaps = 24/129 (18%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIXXXXXXXXXXXXKN 76
G TQ +VG+ALA + G SQ+TICRFE+L LS N LK I
Sbjct: 20 GYTQTNVGEALA--AVHG-SEFSQTTICRFENLQLSFKNACKLKAILSKWL--------- 67
Query: 77 KRRDPDAPSV-------LPAGEKKRKR-TSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEK 128
+A V + A E+KRKR T+I+ K +LE +F +PS ++I +AE+
Sbjct: 68 ----EEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEE 123
Query: 129 LDLKKNVVR 137
L+L+K VVR
Sbjct: 124 LNLEKEVVR 132
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 69.3 bits (168), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 49/122 (40%), Positives = 67/122 (54%), Gaps = 8/122 (6%)
Query: 17 GVTQADVGKALANLKLPGVG-ALSQSTICRFESLTLSHNNMIALKPIXXXXXXXXXXXXK 75
G TQADVG L L G SQ+TI RFE+L LS NM L+P+ +
Sbjct: 27 GYTQADVGLTLGVL----FGKVFSQTTISRFEALQLSLKNMSKLRPLLEKWVEEADNN-E 81
Query: 76 NKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNV 135
N + + +++ A +KRKRTSI + SLE F P+PS ++I IA +L L+K+V
Sbjct: 82 NLQEISKSETLVQA--RKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDV 139
Query: 136 VR 137
VR
Sbjct: 140 VR 141
>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 = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 44/125 (35%), Positives = 66/125 (52%), Gaps = 7/125 (5%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIXXXX----XXXXXX 72
G TQ DVG A+ KL G SQ+TI RFE+L LS NM LKP+
Sbjct: 28 GFTQGDVGLAMG--KLYG-NDFSQTTISRFEALNLSFKNMAKLKPLLEKWLNDAENLSSD 84
Query: 73 XXKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLK 132
+ ++P + E+++KRTSI + +LE F +P+ E+I IA++L+++
Sbjct: 85 SSLSSPSALNSPGIEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNME 144
Query: 133 KNVVR 137
K V+R
Sbjct: 145 KEVIR 149
>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 = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 44/125 (35%), Positives = 64/125 (51%), Gaps = 7/125 (5%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIXXXXXXXXXXXXKN 76
G TQ DVG A+ KL G SQ+TI RFE+L LS NM LKP+ +
Sbjct: 20 GFTQGDVGLAMG--KLYG-NDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAENLSSD 76
Query: 77 KRRDPDAPSVLPAGE----KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLK 132
+ P E +++KRTSI + +LE F +P+ E+I IA++L+++
Sbjct: 77 SSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNME 136
Query: 133 KNVVR 137
K V+R
Sbjct: 137 KEVIR 141
>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 = 66.2 bits (160), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 44/125 (35%), Positives = 64/125 (51%), Gaps = 7/125 (5%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIXXXXXXXXXXXXKN 76
G TQ DVG A+ KL G SQ+TI RFE+L LS NM LKP+ +
Sbjct: 27 GFTQGDVGLAMG--KLYG-NDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAENLSSD 83
Query: 77 KRRDPDAPSVLPAGE----KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLK 132
+ P E +++KRTSI + +LE F +P+ E+I IA++L+++
Sbjct: 84 SSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNME 143
Query: 133 KNVVR 137
K V+R
Sbjct: 144 KEVIR 148
>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 = 65.9 bits (159), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 44/125 (35%), Positives = 64/125 (51%), Gaps = 7/125 (5%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIXXXXXXXXXXXXKN 76
G TQ DVG A+ KL G SQ+TI RFE+L LS NM LKP+ +
Sbjct: 24 GFTQGDVGLAMG--KLYG-NDFSQTTISRFEALNLSFKNMSKLKPLLEKWLNDAENLSSD 80
Query: 77 KRRDPDAPSVLPAGE----KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLK 132
+ P E +++KRTSI + +LE F +P+ E+I IA++L+++
Sbjct: 81 SSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNME 140
Query: 133 KNVVR 137
K V+R
Sbjct: 141 KEVIR 145
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 65.5 bits (158), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 44/126 (34%), Positives = 62/126 (49%), Gaps = 8/126 (6%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIXXXXXXXXXXXXKN 76
G TQ DVG A+ KL G SQ+TI RFE+L LS NM LKP+ +
Sbjct: 24 GFTQGDVGLAMG--KLYG-NDFSQTTISRFEALNLSFKNMSKLKPLLEKWLNDAEANLSS 80
Query: 77 KRRDPDA-----PSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL 131
P + +++KRTSI + +LE F +P+ E I IAE+L++
Sbjct: 81 DSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNM 140
Query: 132 KKNVVR 137
+K V+R
Sbjct: 141 EKEVIR 146
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 38/126 (30%), Positives = 61/126 (48%), Gaps = 3/126 (2%)
Query: 12 RVLFTGVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPIXXXXXXXXX 71
R L G+TQ VG+A + P A SQS I RFE L ++ + LKP+
Sbjct: 16 RRLSLGLTQTQVGQAXTATEGP---AYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAE 72
Query: 72 XXXKNKRRDPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDL 131
+ +++ +K+++RTS +L AYF P P+G++I A++L+
Sbjct: 73 LRNQEGQQNLXEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNY 132
Query: 132 KKNVVR 137
+ VVR
Sbjct: 133 DREVVR 138
>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 = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/46 (54%), Positives = 29/46 (63%), Gaps = 3/46 (6%)
Query: 17 GVTQADVGKALANLKLPGVGALSQSTICRFESLTLSHNNMIALKPI 62
G TQ DVG A+ KL G SQ+TI RFE+L LS NM LKP+
Sbjct: 20 GFTQGDVGLAMG--KLYG-NDFSQTTISRFEALNLSFKNMCKLKPL 62
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 43.1 bits (100), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/46 (50%), Positives = 31/46 (67%)
Query: 92 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137
+KRKRTSI + SLE F P+PS ++I IA +L L+K+VVR
Sbjct: 8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVR 53
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 30/46 (65%)
Query: 92 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137
+++KRTSI + +LE F +P+ E+I IAE+L ++K V+R
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIR 46
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 31/46 (67%)
Query: 92 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137
+++KRTSI + +LE F +P+ E+I IA++L+++K V+R
Sbjct: 7 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIR 52
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 35.0 bits (79), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 30/53 (56%)
Query: 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145
KR RTS + R++++YFA+ P + + +A+K L K V++ + RA
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARA 60
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.7 bits (73), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137
KR RT I + R L YF + PS E+I +A+K L + V++
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52
>pdb|2E19|A Chain A, Solution Structure Of The Homeobox Domain From Human
Nil-2- A Zinc Finger Protein, Transcription Factor 8
Length = 64
Score = 30.4 bits (67), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 24/31 (77%)
Query: 107 LEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 137
L+AY+A+ +PS E+++ IA+ ++L +VV+
Sbjct: 18 LKAYYALNAQPSAEELSKIADSVNLPLDVVK 48
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 26.2 bits (56), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 93 KRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRPINGHTRA 145
KR RT+I + L + + P+ + + IA ++ LKK VV+ +TRA
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRA 70
>pdb|3L1A|A Chain A, Structural Ordering Of Disordered Ligand Binding Loops Of
Biotin Protein Ligase Into Active Conformations As A
Consequence Of Dehydration
pdb|3L1A|B Chain B, Structural Ordering Of Disordered Ligand Binding Loops Of
Biotin Protein Ligase Into Active Conformations As A
Consequence Of Dehydration
pdb|3L2Z|A Chain A, Crystal Structure Of Hydrated Biotin Protein Ligase From
M. Tuberculosis
pdb|3L2Z|B Chain B, Crystal Structure Of Hydrated Biotin Protein Ligase From
M. Tuberculosis
Length = 266
Score = 26.2 bits (56), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 26/89 (29%)
Query: 80 DPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPR----------------------- 116
DPDA S+L G R IA+ R LEA +Q R
Sbjct: 167 DPDATSLLDLGVAAPDRNRIASRLLRELEARI-IQWRNANPQLAADYRARSLTIGSRVRV 225
Query: 117 --PSGEKIAAIAEKLDLKKNVVRPINGHT 143
P G+ + IA +D + + + G T
Sbjct: 226 ELPGGQDVVGIARDIDDQGRLCLDVGGRT 254
>pdb|3RUX|A Chain A, Crystal Structure Of Biotin-Protein Ligase Bira From
Mycobacterium Tuberculosis In Complex With An
Acylsulfamide Bisubstrate Inhibitor
pdb|3RUX|B Chain B, Crystal Structure Of Biotin-Protein Ligase Bira From
Mycobacterium Tuberculosis In Complex With An
Acylsulfamide Bisubstrate Inhibitor
Length = 270
Score = 25.8 bits (55), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 26/89 (29%)
Query: 80 DPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPR----------------------- 116
DPDA S+L G R IA+ R LEA +Q R
Sbjct: 171 DPDATSLLDLGVAAPDRNRIASRLLRELEARI-IQWRNANPQLAADYRARSLTIGSRVRV 229
Query: 117 --PSGEKIAAIAEKLDLKKNVVRPINGHT 143
P G+ + IA +D + + + G T
Sbjct: 230 ELPGGQDVVGIARDIDDQGRLCLDVGGRT 258
>pdb|2CGH|A Chain A, Crystal Structure Of Biotin Ligase From Mycobacterium
Tuberculosis
pdb|2CGH|B Chain B, Crystal Structure Of Biotin Ligase From Mycobacterium
Tuberculosis
Length = 268
Score = 25.8 bits (55), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 26/89 (29%)
Query: 80 DPDAPSVLPAGEKKRKRTSIAAPEKRSLEAYFAVQPR----------------------- 116
DPDA S+L G R IA+ R LEA +Q R
Sbjct: 169 DPDATSLLDLGVAAPDRNRIASRLLRELEARI-IQWRNANPQLAADYRARSLTIGSRVRV 227
Query: 117 --PSGEKIAAIAEKLDLKKNVVRPINGHT 143
P G+ + IA +D + + + G T
Sbjct: 228 ELPGGQDVVGIARDIDDQGRLCLDVGGRT 256
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
0.316 0.132 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,617,962
Number of Sequences: 62578
Number of extensions: 116506
Number of successful extensions: 218
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 191
Number of HSP's gapped (non-prelim): 21
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
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: 47 (22.7 bits)