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= psy3734
(158 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 75.1 bits (183), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 40/61 (65%), Positives = 44/61 (72%), Gaps = 9/61 (14%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNRPVQT 123
PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT L MK+ L + R +Q
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREE--------LAMKIGLTEAR-IQV 52
Query: 124 Y 124
+
Sbjct: 53 W 53
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 62.8 bits (151), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 34/55 (61%), Positives = 39/55 (70%), Gaps = 9/55 (16%)
Query: 70 RYRTTFTSFQLEELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNRPVQTY 124
RYRTTFTSFQLEELEKAFSRTHYPDVFT + L MK+ L + R +Q +
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFT--------REELAMKIGLTEAR-IQVW 46
>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 = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/48 (60%), Positives = 38/48 (79%), Gaps = 1/48 (2%)
Query: 50 EDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
ED+S+ E E +L KRKQRR RTTF++ QL+ELE+AF RT YPD++T
Sbjct: 1 EDISDCESEPGIAL-KRKQRRSRTTFSASQLDELERAFERTQYPDIYT 47
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/58 (51%), Positives = 38/58 (65%), Gaps = 9/58 (15%)
Query: 67 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNRPVQTY 124
K+RR RTTFTS+QLEELEK F +THYPDV+ + L M+ DL + R VQ +
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYA--------REQLAMRTDLTEAR-VQVW 56
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/51 (58%), Positives = 35/51 (68%), Gaps = 9/51 (17%)
Query: 74 TFTSFQLEELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNRPVQTY 124
TFTSFQLEELEKAFSRTHYPDVFT + L MK+ L + R +Q +
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFT--------REELAMKIGLTEAR-IQVW 46
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 23/30 (76%), Positives = 27/30 (90%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
QRR RTTFT+ QLEELE+AF RTHYPD++T
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYT 31
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 33/57 (57%), Gaps = 9/57 (15%)
Query: 70 RYRTTFTSFQLEELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNRPVQTYVA 126
R RT+FT Q+E LEK F RTHYPDVF + L K+DL + R +Q + +
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFA--------RERLAAKIDLPEAR-IQVWFS 56
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/38 (60%), Positives = 26/38 (68%), Gaps = 1/38 (2%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHYPDVFTSTGSIAVF 105
QRR RT FTS QL+ELE F R HYPD+ T IAV+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTR-EEIAVW 39
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/38 (57%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHYPDVFTSTGSIAVF 105
QRR RT FTS QL+ELE F R YPD+ T IAV+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTR-EEIAVW 39
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 17/28 (60%), Positives = 21/28 (75%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHYPDVF 96
RR RTTFT QL+ LE F++T YPD+F
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIF 35
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/29 (62%), Positives = 19/29 (65%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
RR+RT FT QLE LE F T YPDV T
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGT 36
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 31.2 bits (69), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 18/31 (58%)
Query: 62 SLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
S P K RR RT FTS QL ELEK F Y
Sbjct: 1 SAPGGKSRRRRTAFTSEQLLELEKEFHCKKY 31
>pdb|1ZDE|A Chain A, 1.95 Angstrom Crystal Structure Of A Dnae Intein Precursor
From Synechocystis Sp. Pcc 6803
Length = 177
Score = 29.6 bits (65), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 47 RGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSR 89
RGE++V E E+ED + + R+ T T +QL +E+ F+R
Sbjct: 60 RGEQEVLEYELEDGSVIRATSDHRFLT--TDYQLLAIEEIFAR 100
>pdb|1ZD7|A Chain A, 1.7 Angstrom Crystal Structure Of Post-splicing Form Of
A Dnae Intein From Synechocystis Sp. Pcc 6803
pdb|1ZD7|B Chain B, 1.7 Angstrom Crystal Structure Of Post-splicing Form Of
A Dnae Intein From Synechocystis Sp. Pcc 6803
Length = 159
Score = 29.6 bits (65), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 47 RGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSR 89
RGE++V E E+ED + + R+ T T +QL +E+ F+R
Sbjct: 50 RGEQEVLEYELEDGSVIRATSDHRFLT--TDYQLLAIEEIFAR 90
>pdb|3NZM|A Chain A, Crystal Structure Of Dnae Intein With N-Extein In Redox
Trap
Length = 168
Score = 29.3 bits (64), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 47 RGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSR 89
RGE++V E E+ED + + R+ T T +QL +E+ F+R
Sbjct: 59 RGEQEVLEYELEDGSVIRATSDHRFLT--TDYQLLAIEEIFAR 99
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 66 RKQRRYRTTFTSFQLEELEKAFSRTHY---PD 94
+K RR RT FT QL LEK F + Y PD
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPD 46
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHY 92
RRYRT FT QL LEK F + +Y
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENY 25
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 17/24 (70%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHY 92
RR RTTFTS Q+ ELE+ F + Y
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRY 26
>pdb|3OCD|A Chain A, Diheme Soxax - C236m Mutant
pdb|3OCD|C Chain C, Diheme Soxax - C236m Mutant
Length = 275
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 82 ELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNRPVQTYVAY---GTGRKKDLVYR 138
+LE A++ H P F TG + + LL ++ ++ R + VA G GR D+
Sbjct: 82 KLEGAYA--HLPRYFADTGKVMDLEQRLLWCMETIQGRDTKPLVAKPFSGPGRTSDM--- 136
Query: 139 RIEVEIKFIPN 149
E + FI N
Sbjct: 137 --EDLVAFIAN 145
>pdb|3OA8|A Chain A, Diheme Soxax
pdb|3OA8|C Chain C, Diheme Soxax
pdb|3OA8|E Chain E, Diheme Soxax
Length = 275
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 82 ELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNRPVQTYVAY---GTGRKKDLVYR 138
+LE A++ H P F TG + + LL ++ ++ R + VA G GR D+
Sbjct: 82 KLEGAYA--HLPRYFADTGKVMDLEQRLLWCMETIQGRDTKPLVAKPFSGPGRTSDM--- 136
Query: 139 RIEVEIKFIPN 149
E + FI N
Sbjct: 137 --EDLVAFIAN 145
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHY 92
R+ RT ++SFQL L++ F +T Y
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQY 31
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHYPDV 95
RR RT FT Q+E LE F YP +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGI 28
>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 = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
PKRK + RT+FT Q+ ELEK F + Y
Sbjct: 15 PKRK--KPRTSFTRIQVAELEKRFHKQKY 41
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 27.7 bits (60), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHY 92
+RR R T+T +Q ELEK F HY
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHY 44
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
0.318 0.135 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,737,193
Number of Sequences: 62578
Number of extensions: 190704
Number of successful extensions: 399
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 380
Number of HSP's gapped (non-prelim): 28
length of query: 158
length of database: 14,973,337
effective HSP length: 91
effective length of query: 67
effective length of database: 9,278,739
effective search space: 621675513
effective search space used: 621675513
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)