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= psy5909
(130 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 = 78.6 bits (192), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 34/50 (68%), Positives = 43/50 (86%)
Query: 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+K K RRNRTTFT+YQL ELE+ F+K+HYPDVY+RE+LAM+ +L E RVQ
Sbjct: 5 NKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQ 54
>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 = 76.6 bits (187), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 32/49 (65%), Positives = 42/49 (85%)
Query: 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
K+K RR RTTFT++QL ELE+AF ++HYPDV++REELAMK+ L E R+Q
Sbjct: 3 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 51
>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 = 72.8 bits (177), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 31/49 (63%), Positives = 40/49 (81%)
Query: 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
K+K RR+RTTF+ QL ELERAFE++ YPD+Y+REELA + NL E R+Q
Sbjct: 15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 63
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 31/46 (67%), Positives = 37/46 (80%)
Query: 53 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR+RTTFT QL ELERAFE++HYPD+Y+REELA + L E RVQ
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQ 47
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 29/44 (65%), Positives = 38/44 (86%)
Query: 55 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
R RTTFT++QL ELE+AF ++HYPDV++REELAMK+ L E R+Q
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 66.2 bits (160), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 26/40 (65%), Positives = 35/40 (87%)
Query: 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
TFT++QL ELE+AF ++HYPDV++REELAMK+ L E R+Q
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 26/44 (59%), Positives = 36/44 (81%)
Query: 55 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RNRT+FT Q+ LE+ FE++HYPDV++RE LA K++LPE R+Q
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 62.8 bits (151), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 28/45 (62%), Positives = 34/45 (75%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR RTTFT QL LE F K+ YPD++ REE+A+K+NLPE RVQ
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 25/46 (54%), Positives = 34/46 (73%)
Query: 53 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR RT FT+ QL ELE F+++HYPD+ +REE+A+ NL E RV+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVR 48
>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 = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 24/46 (52%), Positives = 33/46 (71%)
Query: 53 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR RT FT+ QL ELE F+++ YPD+ +REE+A+ NL E RV+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 48
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 48.5 bits (114), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/45 (53%), Positives = 33/45 (73%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR+RT FT QL LE F+++ YPDV +RE+LA KV+L E +V+
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 52
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 29/49 (59%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQA 99
KK RR+RT FT QL LE+ FEK Y R +LA + L +++V+
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKT 63
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
K RR RT FT+ QL ELE+ F Y + R ++A + L EV+V+
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVK 52
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 29/45 (64%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
R+ RT ++++QL L+R F+K+ Y + R ELA + L + +V+
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVK 52
>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 = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/41 (51%), Positives = 25/41 (60%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
RR RT FT QL LE+ F K +Y R ELA ++NLPE
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPE 42
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 26/45 (57%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR RT FT Q+ LE F + YP + E+LA K+NL R+Q
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
R+ RT FTT QL LER F + Y + R E + ++L E +V+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK 45
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR R T+T YQ ELE+ F +HY R E+A ++L E +++
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIK 65
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 32.0 bits (71), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 24/42 (57%)
Query: 57 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RT FTT QL ELE+ F + Y R E+A + L E +V+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK 79
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 32.0 bits (71), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR RTTFT+ Q+ ELE+ F + Y +L+ K+ L +V+
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVK 47
>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 = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 53 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
++R RT +T QL ELE+ F + Y R ELA+ +NL E
Sbjct: 3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTE 44
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+R RT+F +QL ++ F +H PD ++LA K L + +Q
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52
>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 = 0.41, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
K ++ RT+FT Q+ ELE+ F K Y R LA + + + +V+
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVK 62
>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 = 29.6 bits (65), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+R RT++T YQ ELE+ F + Y R E+A ++L E +++
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 73
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 29.3 bits (64), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 58 TTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGM 102
T FT YQL L+ F+ + YP E+L+ +NLP RV V
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLP-TRVIVVWF 55
>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 = 28.9 bits (63), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+R R T+T YQ ELE+ F + Y R E+A ++L E +++
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 47
>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 = 16/45 (35%), Positives = 26/45 (57%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+R R T+T YQ ELE+ F + Y R E+A ++L E +++
Sbjct: 4 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 48
>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 = 1.4, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+R R T+T YQ ELE+ F + Y R E+A + L E +++
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 47
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The
Fushi Tarazu Homeodomain From Drosophila And Comparison
With The Antennapedia Homeodomain
Length = 70
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+R R T+T YQ ELE+ F + Y R ++A ++L E +++
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIK 48
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNL 92
K ++ RT F++ QL L F++ Y + +EL+ +NL
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 57 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
RT F+ QL L+ F+K Y + +EL+ +NL +V
Sbjct: 7 RTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQV 47
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
R+ R +T YQ ELE+ F + Y R E+A +NL E +V+
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVK 46
>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 = 25.4 bits (54), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 59 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
T+T YQ ELE+ F + Y R E+A ++L E +++
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 41
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
0.312 0.130 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,517,014
Number of Sequences: 62578
Number of extensions: 117451
Number of successful extensions: 171
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 133
Number of HSP's gapped (non-prelim): 42
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)