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= psy9533
(73 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 13/14 (92%), Positives = 14/14 (100%)
Query: 4 VWFQNRRAKWRKKE 17
VWFQNRRAKWRK+E
Sbjct: 55 VWFQNRRAKWRKRE 68
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 13/14 (92%), Positives = 14/14 (100%)
Query: 4 VWFQNRRAKWRKKE 17
VWFQNRRAKWRK+E
Sbjct: 45 VWFQNRRAKWRKQE 58
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 13/14 (92%), Positives = 14/14 (100%)
Query: 4 VWFQNRRAKWRKKE 17
VWFQNRRAKWRK+E
Sbjct: 45 VWFQNRRAKWRKQE 58
>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 = 33.1 bits (74), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 13/14 (92%), Positives = 14/14 (100%)
Query: 4 VWFQNRRAKWRKKE 17
VWFQNRRAKWRK+E
Sbjct: 52 VWFQNRRAKWRKQE 65
>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 = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 4 VWFQNRRAKWRKKEHTKKGPG 24
+WFQNRR KW+K+ TK PG
Sbjct: 42 IWFQNRRMKWKKENKTKGEPG 62
>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 = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 4 VWFQNRRAKWRKKEHTKKGPG 24
+WFQNRR KW+K+ TK PG
Sbjct: 48 IWFQNRRMKWKKENKTKGEPG 68
>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 = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 4 VWFQNRRAKWRKKEHTKKGPG 24
+WFQNRR KW+K+ TK PG
Sbjct: 48 IWFQNRRMKWKKENKTKGEPG 68
>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 = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 4 VWFQNRRAKWRKKEH 18
VWF+NRRAKWRK+E
Sbjct: 49 VWFKNRRAKWRKREE 63
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 12/14 (85%), Positives = 14/14 (100%)
Query: 4 VWFQNRRAKWRKKE 17
VWF+NRRAKWRK+E
Sbjct: 49 VWFKNRRAKWRKRE 62
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 4 VWFQNRRAKWRKKE 17
VWF NRRAKWR++E
Sbjct: 53 VWFSNRRAKWRREE 66
>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 = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 4 VWFQNRRAKWRKKEHTKKGPGRPAHN 29
WFQNRR KWR++ ++ R A N
Sbjct: 63 TWFQNRRTKWRRQTAEEREAERQAAN 88
>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 = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 4 VWFQNRRAKWRKKE 17
+WFQNRR KW+K+E
Sbjct: 49 IWFQNRRMKWKKEE 62
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 10/12 (83%), Positives = 12/12 (100%)
Query: 4 VWFQNRRAKWRK 15
VWF+NRRAKWR+
Sbjct: 53 VWFKNRRAKWRR 64
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 28.5 bits (62), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 9/12 (75%), Positives = 12/12 (100%)
Query: 4 VWFQNRRAKWRK 15
+WFQNRRAKW++
Sbjct: 53 IWFQNRRAKWKR 64
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 4 VWFQNRRAKWRKK 16
VWF NRRA+WRK+
Sbjct: 48 VWFSNRRARWRKQ 60
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 28.1 bits (61), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/12 (83%), Positives = 11/12 (91%)
Query: 4 VWFQNRRAKWRK 15
WFQNRRAKWR+
Sbjct: 53 TWFQNRRAKWRR 64
>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 = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 13/15 (86%), Gaps = 1/15 (6%)
Query: 4 VWFQNRRAKWRKKEH 18
+WFQNRR KW KKEH
Sbjct: 74 IWFQNRRMKW-KKEH 87
>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 = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/16 (75%), Positives = 14/16 (87%), Gaps = 1/16 (6%)
Query: 4 VWFQNRRAKWRKKEHT 19
VWFQNRRA+ RK+ HT
Sbjct: 64 VWFQNRRARLRKQ-HT 78
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 4 VWFQNRRAKWRKK 16
WFQNRR KWR++
Sbjct: 43 TWFQNRRTKWRRQ 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 = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 4 VWFQNRRAKWRKK 16
+WFQNRR KW+K+
Sbjct: 5 IWFQNRRMKWKKR 17
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 4 VWFQNRRAKWRKK 16
+WFQNRR KW+K+
Sbjct: 49 IWFQNRRMKWKKE 61
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 25.8 bits (55), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 4 VWFQNRRAKWRK 15
+WFQNRR KW+K
Sbjct: 5 IWFQNRRMKWKK 16
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 25.8 bits (55), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 4 VWFQNRRAKWRK 15
+WFQNRR KW+K
Sbjct: 5 IWFQNRRMKWKK 16
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 25.4 bits (54), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 4 VWFQNRRAKWRK 15
W+QNRR KW+K
Sbjct: 63 TWYQNRRMKWKK 74
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 25.4 bits (54), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 4 VWFQNRRAKWRKKEH 18
+WFQNRR K +K+E
Sbjct: 80 IWFQNRRMKQKKRER 94
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
0.319 0.134 0.452
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,918,722
Number of Sequences: 62578
Number of extensions: 44471
Number of successful extensions: 118
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 90
Number of HSP's gapped (non-prelim): 28
length of query: 73
length of database: 14,973,337
effective HSP length: 43
effective length of query: 30
effective length of database: 12,282,483
effective search space: 368474490
effective search space used: 368474490
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)