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= psy5351
(65 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
Length = 93
Score = 33.1 bits (74), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 13/19 (68%), Positives = 16/19 (84%)
Query: 2 VEVWFQNRRTKWRKKHAAE 20
V+ WFQNRRTKWR++ A E
Sbjct: 61 VKTWFQNRRTKWRRQTAEE 79
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 2 VEVWFQNRRTKWRKK 16
V+VWFQNRR KWRK+
Sbjct: 53 VQVWFQNRRAKWRKR 67
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 10/16 (62%), Positives = 15/16 (93%)
Query: 2 VEVWFQNRRTKWRKKH 17
+++WFQNRR KW+K+H
Sbjct: 72 IKIWFQNRRMKWKKEH 87
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 14/15 (93%)
Query: 2 VEVWFQNRRTKWRKK 16
++VWFQNRR KWRK+
Sbjct: 43 IQVWFQNRRAKWRKQ 57
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 14/15 (93%)
Query: 2 VEVWFQNRRTKWRKK 16
++VWFQNRR KWRK+
Sbjct: 43 IQVWFQNRRAKWRKQ 57
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
Length = 67
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 2 VEVWFQNRRTKWRKKH 17
++VWFQNRR KWRK+
Sbjct: 50 IQVWFQNRRAKWRKQE 65
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 14/15 (93%)
Query: 2 VEVWFQNRRTKWRKK 16
V+ WFQNRRTKWR++
Sbjct: 41 VKTWFQNRRTKWRRQ 55
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 2 VEVWFQNRRTKWRKKHAA 19
VEVWF+NRR KWR+ +
Sbjct: 51 VEVWFKNRRAKWRRSGPS 68
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
Length = 81
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 2 VEVWFQNRRTKWRKKHAA 19
++VWFQNRR + RK+H +
Sbjct: 62 IQVWFQNRRARLRKQHTS 79
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 29.3 bits (64), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 2 VEVWFQNRRTKWRKKHAAEMA 22
V++WFQNRR KW++ A ++
Sbjct: 51 VKIWFQNRRAKWKRIKAGNVS 71
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex
With Dna
pdb|2H1K|B Chain B, Crystal Structure Of The Pdx1 Homeodomain In Complex
With Dna
Length = 63
Score = 28.5 bits (62), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 2 VEVWFQNRRTKWRKK 16
+++WFQNRR KW+K+
Sbjct: 47 IKIWFQNRRMKWKKE 61
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 2 VEVWFQNRRTKWRKKHAA 19
V+ WFQNRR KWR+ +
Sbjct: 51 VKTWFQNRRAKWRRSGPS 68
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 2 VEVWFQNRRTKWRKKH 17
++VWF NRR KWR++
Sbjct: 51 IQVWFSNRRAKWRREE 66
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The
Nmr Solution Structure And The Dna Binding Affinity
With The Intact Antennapedia Homeodomain
Length = 62
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 15/16 (93%)
Query: 2 VEVWFQNRRTKWRKKH 17
+++WFQNRR KW+K++
Sbjct: 40 IKIWFQNRRMKWKKEN 55
>pdb|2NZZ|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
pdb|2O00|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
Length = 37
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 2 VEVWFQNRRTKWRKK 16
+++WFQNRR KW+K+
Sbjct: 3 IKIWFQNRRMKWKKR 17
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The
Antennapedia Homeodomain From Drosophila In Solution By
1h Nuclear Magnetic Resonance Spectroscopy
Length = 68
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 2 VEVWFQNRRTKWRKKHAA 19
+++WFQNRR KW+K++
Sbjct: 46 IKIWFQNRRMKWKKENKT 63
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex
With A Taatcc Dna Binding Site
Length = 68
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 2 VEVWFQNRRTKWRKKH 17
V VWF+NRR KWRK+
Sbjct: 47 VRVWFKNRRAKWRKRE 62
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An
Antennapedia Homeodomain-Dna Complex
pdb|2HOA|A Chain A, Structure Determination Of The Antp(C39->s) Homeodomain
From Nuclear Magnetic Resonance Data In Solution Using
A Novel Strategy For The Structure Calculation With The
Programs Diana, Caliba, Habas And Glomsa
Length = 68
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 2 VEVWFQNRRTKWRKKHAA 19
+++WFQNRR KW+K++
Sbjct: 46 IKIWFQNRRMKWKKENKT 63
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 2 VEVWFQNRRTKWRKK 16
V VWF+NRR KWRK+
Sbjct: 47 VRVWFKNRRAKWRKR 61
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 2 VEVWFQNRRTKWRKK 16
V+VWF NRR +WRK+
Sbjct: 46 VQVWFSNRRARWRKQ 60
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 15/16 (93%)
Query: 2 VEVWFQNRRTKWRKKH 17
+++WFQNRR KW+K++
Sbjct: 47 IKIWFQNRRMKWKKEN 62
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 2 VEVWFQNRRTKWRK 15
+++WFQNRR KW+K
Sbjct: 3 IKIWFQNRRMKWKK 16
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 2 VEVWFQNRRTKWRKKHAA 19
V+ W+QNRR KW+K +
Sbjct: 61 VKTWYQNRRMKWKKSGPS 78
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 2 VEVWFQNRRTKWRK 15
+++WFQNRR KW+K
Sbjct: 3 IKIWFQNRRMKWKK 16
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 2 VEVWFQNRRTKWRKKH 17
+++WFQNRR K ++ H
Sbjct: 45 IQIWFQNRRAKLKRSH 60
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 25.0 bits (53), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 2 VEVWFQNRRTKWRKKHAA 19
V++WFQNRR K ++K +
Sbjct: 48 VKIWFQNRRYKTKRKQLS 65
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
0.321 0.125 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,533,734
Number of Sequences: 62578
Number of extensions: 31081
Number of successful extensions: 108
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 77
Number of HSP's gapped (non-prelim): 31
length of query: 65
length of database: 14,973,337
effective HSP length: 36
effective length of query: 29
effective length of database: 12,720,529
effective search space: 368895341
effective search space used: 368895341
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)