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= psy10196
(354 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 = 6e-15, Method: Compositional matrix adjust.
Identities = 34/50 (68%), Positives = 43/50 (86%)
Query: 67 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
+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 = 75.9 bits (185), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 32/49 (65%), Positives = 42/49 (85%)
Query: 68 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
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 = 3e-13, Method: Compositional matrix adjust.
Identities = 35/60 (58%), Positives = 44/60 (73%), Gaps = 2/60 (3%)
Query: 68 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ--FTALAAALR 125
K+K RR+RTTF+ QL ELERAFE++ YPD+Y+REELA + NL E R+Q F A LR
Sbjct: 15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 31/46 (67%), Positives = 37/46 (80%)
Query: 71 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
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 = 67.8 bits (164), Expect = 8e-12, Method: Composition-based stats.
Identities = 29/44 (65%), Positives = 38/44 (86%)
Query: 73 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
R RTTFT++QL ELE+AF ++HYPDV++REELAMK+ L E R+Q
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 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 = 5e-11, Method: Compositional matrix adjust.
Identities = 26/44 (59%), Positives = 36/44 (81%)
Query: 73 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
RNRT+FT Q+ LE+ FE++HYPDV++RE LA K++LPE R+Q
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 63.9 bits (154), Expect = 1e-10, Method: Composition-based stats.
Identities = 26/40 (65%), Positives = 35/40 (87%)
Query: 77 TFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
TFT++QL ELE+AF ++HYPDV++REELAMK+ L E R+Q
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 28/45 (62%), Positives = 34/45 (75%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/57 (50%), Positives = 37/57 (64%), Gaps = 2/57 (3%)
Query: 71 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE--VRVQFTALAAALR 125
RR RT FT+ QL ELE F+++HYPD+ +REE+A+ NL E VRV F A R
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWR 59
>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 = 2e-07, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 36/57 (63%), Gaps = 2/57 (3%)
Query: 71 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE--VRVQFTALAAALR 125
RR RT FT+ QL ELE F+++ YPD+ +REE+A+ NL E VRV F A R
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWR 59
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/45 (53%), Positives = 33/45 (73%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
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 = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 29/48 (60%)
Query: 69 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
KK RR+RT FT QL LE+ FEK Y R +LA + L +++V+
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVK 62
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 20/47 (42%), Positives = 28/47 (59%)
Query: 70 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
K RR RT FT+ QL ELE+ F Y + R ++A + L EV+V+
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVK 52
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 20/45 (44%), Positives = 26/45 (57%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
RR RT FT Q+ LE F + YP + E+LA K+NL R+Q
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
RR R T+T YQ ELE+ F +HY R E+A ++L E +++
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIK 65
>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 = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE--VRVQF 117
RR RT FT QL LE+ F K +Y R ELA ++NLPE ++V F
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWF 49
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 35.8 bits (81), Expect = 0.041, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 29/45 (64%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
R+ RT ++++QL L+R F+K+ Y + R ELA + L + +V+
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVK 52
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 35.0 bits (79), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
R+ RT FTT QL LER F + Y + R E + ++L E +V+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK 45
>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 = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 71 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
++R RT +T QL ELE+ F + Y R ELA+ +NL E ++
Sbjct: 3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIK 48
>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 = 32.3 bits (72), Expect = 0.38, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
+R RT++T YQ ELE+ F + Y R E+A ++L E +++
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 73
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 24/42 (57%)
Query: 75 RTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
RT FTT QL ELE+ F + Y R E+A + L E +V+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK 79
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 32.0 bits (71), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE--VRVQFTALAAALR 125
+R RT+F +QL ++ F +H PD ++LA K L + ++V F A R
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 31.6 bits (70), Expect = 0.64, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 70 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
+ +R R T+T YQ ELE+ F + Y R E+A ++L E +++
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 48
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNL--PEVRVQF 117
RR RTTFT+ Q+ ELE+ F + Y +L+ K+ L +V++ F
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWF 50
>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 = 31.2 bits (69), Expect = 0.91, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
+R R T+T YQ ELE+ F + Y R E+A ++L E +++
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 47
>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 = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
+R R T+T YQ ELE+ F + Y R E+A + L E +++
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 47
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 76 TTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLP 111
T FT YQL L+ F+ + YP E+L+ +NLP
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLP 47
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
R+ R +T YQ ELE+ F + Y R E+A +NL E +V+
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVK 46
>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 = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 70 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
K ++ RT+FT Q+ ELE+ F K Y R LA + + + +V+
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVK 62
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
0.315 0.131 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,676,742
Number of Sequences: 62578
Number of extensions: 309531
Number of successful extensions: 636
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 606
Number of HSP's gapped (non-prelim): 31
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)