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= psy15889
(92 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/29 (68%), Positives = 22/29 (75%), Gaps = 5/29 (17%)
Query: 3 ELMALWL-----RVRVWFKNRRAKWRKRE 26
E +A+W RVRVWFKNRRAKWRKRE
Sbjct: 34 EEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/29 (68%), Positives = 22/29 (75%), Gaps = 5/29 (17%)
Query: 3 ELMALWL-----RVRVWFKNRRAKWRKRE 26
E +A+W RVRVWFKNRRAKWRKRE
Sbjct: 34 EEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/18 (88%), Positives = 18/18 (100%)
Query: 10 RVRVWFKNRRAKWRKRER 27
RV+VWF+NRRAKWRKRER
Sbjct: 52 RVQVWFQNRRAKWRKRER 69
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 13/18 (72%), Positives = 18/18 (100%)
Query: 10 RVRVWFKNRRAKWRKRER 27
R++VWF+NRRAKWRK+E+
Sbjct: 42 RIQVWFQNRRAKWRKQEK 59
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 34.3 bits (77), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 13/17 (76%), Positives = 17/17 (100%)
Query: 10 RVRVWFKNRRAKWRKRE 26
R++VWF+NRRAKWRK+E
Sbjct: 42 RIQVWFQNRRAKWRKQE 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 = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 13/18 (72%), Positives = 18/18 (100%)
Query: 10 RVRVWFKNRRAKWRKRER 27
R++VWF+NRRAKWRK+E+
Sbjct: 49 RIQVWFQNRRAKWRKQEK 66
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 32.0 bits (71), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 12/18 (66%), Positives = 16/18 (88%)
Query: 10 RVRVWFKNRRAKWRKRER 27
R++VWF NRRAKWR+ E+
Sbjct: 50 RIQVWFSNRRAKWRREEK 67
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 10 RVRVWFKNRRAKWRK 24
+V VWFKNRRAKWR+
Sbjct: 50 KVEVWFKNRRAKWRR 64
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 10 RVRVWFKNRRAKWRK 24
RV+VWF NRRA+WRK
Sbjct: 45 RVQVWFSNRRARWRK 59
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 16/28 (57%), Positives = 19/28 (67%), Gaps = 5/28 (17%)
Query: 1 MGELMALWL-----RVRVWFKNRRAKWR 23
M E +AL + RV+VWFKNRRAK R
Sbjct: 36 MREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 16/18 (88%)
Query: 10 RVRVWFKNRRAKWRKRER 27
+V++WF+NRR K +KRER
Sbjct: 77 QVKIWFQNRRMKQKKRER 94
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 28.9 bits (63), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 16/16 (100%)
Query: 9 LRVRVWFKNRRAKWRK 24
++V++WF+NRRAKW++
Sbjct: 49 VQVKIWFQNRRAKWKR 64
>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 = 1.0, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 19/25 (76%), Gaps = 1/25 (4%)
Query: 1 MGELMALWLR-VRVWFKNRRAKWRK 24
+ +++ L R V+ WF+NRRAKWR+
Sbjct: 40 LAKMLQLSERQVKTWFQNRRAKWRR 64
>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 = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 11 VRVWFKNRRAKWRKRE 26
+++WF+NRR KW+K E
Sbjct: 47 IKIWFQNRRMKWKKEE 62
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 14/15 (93%)
Query: 10 RVRVWFKNRRAKWRK 24
R++VWF+NRRA+ RK
Sbjct: 61 RIQVWFQNRRARLRK 75
>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 = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 11 VRVWFKNRRAKWRKR 25
+++WF+NRR KW+KR
Sbjct: 3 IKIWFQNRRMKWKKR 17
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 9 LRVRVWFKNRRAKWRK 24
L+V+ W++NRR KW+K
Sbjct: 59 LQVKTWYQNRRMKWKK 74
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 10 RVRVWFKNRRAKWRKRER 27
R+++WF+NRRAK ++ R
Sbjct: 44 RIQIWFQNRRAKLKRSHR 61
>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 = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 VRVWFKNRRAKWRK 24
+++WF+NRR KW+K
Sbjct: 40 IKIWFQNRRMKWKK 53
>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 = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 11 VRVWFKNRRAKWRKRER 27
+++WF+NRR KW+K +
Sbjct: 72 IKIWFQNRRMKWKKEHK 88
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 11 VRVWFKNRRAKWRK 24
V+ WF+NRR KWR+
Sbjct: 41 VKTWFQNRRTKWRR 54
>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 = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 11 VRVWFKNRRAKWRK 24
V+ WF+NRR KWR+
Sbjct: 61 VKTWFQNRRTKWRR 74
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 VRVWFKNRRAKWRK 24
+++WF+NRR KW+K
Sbjct: 47 IKIWFQNRRMKWKK 60
>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 = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 VRVWFKNRRAKWRK 24
+++WF+NRR KW+K
Sbjct: 46 IKIWFQNRRMKWKK 59
>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 = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 VRVWFKNRRAKWRK 24
+++WF+NRR KW+K
Sbjct: 46 IKIWFQNRRMKWKK 59
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 25.4 bits (54), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 11 VRVWFKNRRAKWRKR 25
+RVWF+N+R K +KR
Sbjct: 47 IRVWFQNKRCKDKKR 61
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 25.0 bits (53), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 VRVWFKNRRAKWRK 24
+++WF+NRR KW+K
Sbjct: 3 IKIWFQNRRMKWKK 16
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 0.134 0.432
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,681,768
Number of Sequences: 62578
Number of extensions: 82987
Number of successful extensions: 205
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 173
Number of HSP's gapped (non-prelim): 32
length of query: 92
length of database: 14,973,337
effective HSP length: 59
effective length of query: 33
effective length of database: 11,281,235
effective search space: 372280755
effective search space used: 372280755
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)