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= psy3735
(91 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 = 75.5 bits (184), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 35/36 (97%), Positives = 36/36 (100%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR+
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRE 37
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 29/30 (96%), Positives = 30/30 (100%)
Query: 31 RYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
RYRTTFTSFQLEELEKAFSRTHYPDVFTR+
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTRE 30
>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 = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/50 (60%), Positives = 40/50 (80%), Gaps = 1/50 (2%)
Query: 11 EDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
ED+S+ E E +L KRKQRR RTTF++ QL+ELE+AF RT YPD++TR+
Sbjct: 1 EDISDCESEPGIAL-KRKQRRSRTTFSASQLDELERAFERTQYPDIYTRE 49
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 25/26 (96%), Positives = 26/26 (100%)
Query: 35 TFTSFQLEELEKAFSRTHYPDVFTRQ 60
TFTSFQLEELEKAFSRTHYPDVFTR+
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTRE 30
>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 = 8e-09, Method: Compositional matrix adjust.
Identities = 24/33 (72%), Positives = 29/33 (87%)
Query: 28 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
K+RR RTTFTS+QLEELEK F +THYPDV+ R+
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYARE 40
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/32 (75%), Positives = 29/32 (90%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
QRR RTTFT+ QLEELE+AF RTHYPD++TR+
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTRE 33
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 47.0 bits (110), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 31 RYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86
R RT+FT Q+E LEK F RTHYPDVF R+ R + + +P W + A +
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARE--RLAAKIDLPEARIQVWFSNRRAKW 62
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/32 (65%), Positives = 24/32 (75%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
QRR RT FTS QL+ELE F R HYPD+ TR+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTRE 34
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/31 (58%), Positives = 23/31 (74%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
RR RTTFT QL+ LE F++T YPD+F R+
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMRE 38
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/32 (62%), Positives = 23/32 (71%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
QRR RT FTS QL+ELE F R YPD+ TR+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTRE 34
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS 89
RR+RT FT QLE LE F T YPDV TR+ + +R+ + E W + A + S
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTRE--QLARKVHLREEKVEVWFKNRRAKWRRS 65
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/37 (51%), Positives = 20/37 (54%)
Query: 23 SLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
S P K RR RT FTS QL ELEK F Y + R
Sbjct: 1 SAPGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTER 37
>pdb|1ZDE|A Chain A, 1.95 Angstrom Crystal Structure Of A Dnae Intein Precursor
From Synechocystis Sp. Pcc 6803
Length = 177
Score = 30.0 bits (66), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 8 RGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSR 50
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 = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 8 RGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSR 50
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 = 29.6 bits (65), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 2/43 (4%)
Query: 8 RGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSR 50
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 = 0.58, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 27 RKQRRYRTTFTSFQLEELEKAFSRTHY---PD 55
+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 = 0.72, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHH 81
RRYRT FT QL LEK F + +Y R+C + Q ++P W +
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSR-PRRCE-LAAQLNLPESTIKVWFQN 51
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHY 53
R+ RT ++SFQL L++ F +T Y
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQY 31
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 17/24 (70%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHY 53
RR RTTFTS Q+ ELE+ F + Y
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRY 26
>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 = 1.2, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
PKRK + RT+FT Q+ ELEK F + Y
Sbjct: 15 PKRK--KPRTSFTRIQVAELEKRFHKQKY 41
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDV 56
RR RT FT Q+E LE F YP +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGI 28
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 26.9 bits (58), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHY 53
+RR R T+T +Q ELEK F HY
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHY 44
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF 86
+R RT+F QL ++ F+ H PD + + +++ + + W + A F
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDA--KDLKQLAQKTGLTKRVLQVWFQNARAKF 62
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 34 TTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHH 81
T FT +QL L+ F YP + + S ++P + V W +
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPK--DDEFEQLSNLLNLPTRVIVVWFQN 57
>pdb|2HBO|A Chain A, Crystal Structure Of A Thioesterase Superfamily Protein
(Cc_3309) From Caulobacter Vibrioides At 1.85 A
Resolution
Length = 158
Score = 25.8 bits (55), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 36 FTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAW---THHLNA 84
T Q + + FS+ ++ F RQ G R PG+ +A+ HH N
Sbjct: 6 LTDAQTAAIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRVEEHHTNG 57
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 0.130 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,871,413
Number of Sequences: 62578
Number of extensions: 95042
Number of successful extensions: 214
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 194
Number of HSP's gapped (non-prelim): 29
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)