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= psy3396
(128 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 66.6 bits (161), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 31/50 (62%), Positives = 38/50 (76%), Gaps = 7/50 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAI-------LFQVWFQNRRAKYRKQEK 44
QL ELE AF+++HYPD++ REELA+ QVWFQNRRAK+RKQEK
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>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 = 66.2 bits (160), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 31/50 (62%), Positives = 38/50 (76%), Gaps = 7/50 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAI-------LFQVWFQNRRAKYRKQEK 44
QL ELE AF+++HYPD++ REELA+ QVWFQNRRAK+RKQEK
Sbjct: 17 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/49 (61%), Positives = 37/49 (75%), Gaps = 7/49 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAI-------LFQVWFQNRRAKYRKQE 43
QL ELE AF+++HYPD++ REELA+ QVWFQNRRAK+RKQE
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 62.8 bits (151), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 29/50 (58%), Positives = 36/50 (72%), Gaps = 7/50 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAI-------LFQVWFQNRRAKYRKQEK 44
QL ELE F K+HYPD+Y RE+LA+ QVWFQNRRAK+RK+E+
Sbjct: 20 QLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER 69
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 30/49 (61%), Positives = 34/49 (69%), Gaps = 7/49 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRKQ 42
EQL ELE AF ++HYPDIY REELA QVWF NRRA++RKQ
Sbjct: 12 EQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>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 = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/48 (60%), Positives = 32/48 (66%), Gaps = 7/48 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRKQ 42
QL ELE AF ++ YPDIY REELA QVWFQNRRA+ RKQ
Sbjct: 29 QLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 26/51 (50%), Positives = 37/51 (72%), Gaps = 7/51 (13%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAIL-------FQVWFQNRRAKYRKQEK 44
+QL ELEA F ++HYPD+ REE+A+ +VWF+NRRAK+RK+E+
Sbjct: 13 QQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 33/51 (64%), Gaps = 7/51 (13%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRKQEK 44
EQ+ LE F ++HYPD++ RE LA QVWF NRRAK+R++EK
Sbjct: 17 EQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 36/51 (70%), Gaps = 7/51 (13%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAIL-------FQVWFQNRRAKYRKQEK 44
+QL ELEA F ++ YPD+ REE+A+ +VWF+NRRAK+RK+E+
Sbjct: 13 QQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 31/46 (67%), Gaps = 7/46 (15%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYR 40
QL LEA FAK+ YPDI+ REE+A+ QVWF+NRRAK R
Sbjct: 18 QLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 30/48 (62%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAI-------LFQVWFQNRRAKYRK 41
EQL LE F ++ YPD+ RE+LA +VWF+NRRAK+R+
Sbjct: 17 EQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
QL +++ FA +H PD ++LA + QVWFQN RAK+R+
Sbjct: 18 QLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 7/49 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQE 43
QL ELE F + Y R ELA++ ++WFQNRR K++K+E
Sbjct: 14 QLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
EQL ELE F Y + R ++A + ++WFQNRRAK+++
Sbjct: 17 EQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 28/53 (52%), Gaps = 7/53 (13%)
Query: 2 QLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRKQEKQLQ 47
Q+ LE F + YP I E+LA Q+WFQNRRAK ++ ++ Q
Sbjct: 12 QIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ 64
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILFQ-------VWFQNRRAKYRKQEKQ 45
QL ELE F + Y R E+A + +WFQNRR K +K+E++
Sbjct: 45 QLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAILFQV-------WFQNRRAKYRK 41
+Q ELE F Y R+ LA + Q+ WFQNRRAK+R+
Sbjct: 17 DQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 33.1 bits (74), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRK 41
QLA L+ F K+ Y + R ELA ++WFQN+R+K +K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>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 = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRKQ 42
Q+AELE F K Y R LA + WFQNRR K+R+Q
Sbjct: 28 QVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
>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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 7/49 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAIL-------FQVWFQNRRAKYRKQ 42
+QL L +A + PD +E+L + +VWFQN+R K +K+
Sbjct: 13 KQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
>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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELAI-------LFQVWFQNRRAKYRKQ 42
+QL LE F K +Y R ELA +VWFQNRR K ++Q
Sbjct: 11 DQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
EQLA L+ F ++ Y R++L+ ++WFQN+RAK +K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
EQLA L+ F ++ Y R++L+ ++WFQN+RAK +K
Sbjct: 13 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQ 42
Q ELE F +HY R E+A ++WFQNRR K +K+
Sbjct: 31 QTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 30.0 bits (66), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILFQV-------WFQNRRAKYRKQ 42
Q+ ELE F + Y R LA ++ WFQNRR K+R+Q
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
QL LE F + Y I R E + ++WFQNRRAK ++
Sbjct: 11 QLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>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 = 0.62, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHY---PD-IYCREELAIL---FQVWFQNRRAKYRK 41
QL LE F K Y PD I E L + + W+QNRR K++K
Sbjct: 28 QLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>pdb|2IXT|A Chain A, Sphericase
pdb|2IXT|B Chain B, Sphericase
pdb|3D43|A Chain A, The Crystal Structure Of Sph At 0.8a
pdb|3D43|B Chain B, The Crystal Structure Of Sph At 0.8a
Length = 310
Score = 29.3 bits (64), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 3/57 (5%)
Query: 70 TSRGYQPYPHPNTINRQHFVILVPGMSTEDEWYNK---SLSALRMNSSHHSNLATPM 123
+SRGY I I PG S WYN ++S M + H S LA +
Sbjct: 207 SSRGYISTAGDYVIQEGDIEISAPGSSVYSTWYNGGYNTISGTSMATPHVSGLAAKI 263
>pdb|3H6E|A Chain A, The Crystal Structure Of A Carbohydrate Kinase From
Novosphingobium Aromaticivorans
pdb|3H6E|B Chain B, The Crystal Structure Of A Carbohydrate Kinase From
Novosphingobium Aromaticivorans
Length = 482
Score = 28.9 bits (63), Expect = 0.70, Method: Composition-based stats.
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 64 RNIYPTTSRGYQPYPH 79
R I PT RG+ PYPH
Sbjct: 336 RXILPTLXRGFGPYPH 351
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 28.9 bits (63), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
EQLA L+ F ++ Y R++L+ ++WFQN RAK +K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|1EA7|A Chain A, Sphericase
Length = 310
Score = 28.9 bits (63), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 3/57 (5%)
Query: 70 TSRGYQPYPHPNTINRQHFVILVPGMSTEDEWYNK---SLSALRMNSSHHSNLATPM 123
+SRGY I I PG S WYN ++S M + H S LA +
Sbjct: 207 SSRGYISTAGDYVIQEGDIEISAPGSSVYSTWYNGGYNTISGTXMATPHVSGLAAKI 263
>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 = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQEK 44
Q ELE F + Y R E+A ++WFQNRR K++K+ K
Sbjct: 39 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 28.9 bits (63), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
EQLA L+ F ++ Y R++L+ ++WF+N+RAK +K
Sbjct: 13 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 2 QLAELEAAFAKSHY------PDIYCREELAIL-FQVWFQNRRAKYRKQEKQ 45
Q+AELE F + Y D+ + L ++WF+NRR +++ Q Q
Sbjct: 13 QIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 63
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
EQLA L+ F ++ Y R++L+ ++WFQN RAK +K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 7/45 (15%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAK 38
EQLA L+ F ++ Y R++L+ ++WFQN+RAK
Sbjct: 9 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
EQLA + F ++ Y R++L+ ++WFQN+RAK R+
Sbjct: 13 EQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>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 = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQEK 44
Q ELE F + Y R E+A ++WFQNRR K++K+ K
Sbjct: 7 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQEK 44
Q+ ELE F + Y RE LA + ++WFQN R K ++Q K
Sbjct: 13 QVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
>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 = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQEK 44
Q ELE F + Y R E+A ++WFQNRR K++K+ K
Sbjct: 13 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
>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 = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQEK 44
Q ELE F + Y R E+A ++WFQNRR K++K+ K
Sbjct: 13 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILFQ-------VWFQNRRAK 38
Q+ ELE F + Y R++LA + + +WFQNRR K
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 7/48 (14%)
Query: 1 EQLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRK 41
EQLA L+ F ++ Y R++L+ ++WF N+RAK +K
Sbjct: 9 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|1EO2|B Chain B, Crystal Structure Of Acinetobacter Sp. Adp1
Protocatechuate 3,4- Dioxygenase
pdb|1EO9|B Chain B, Crystal Structure Of Acinetobacter Sp. Adp1
Protocatechuate 3,4- Dioxygenase At Ph < 7.0
pdb|1EOA|B Chain B, Crystal Structure Of Acinetobacter Sp. Adp1
Protocatechuate 3,4- Dioxygenase In Complex With Cyanide
pdb|1EOB|B Chain B, Crystal Structure Of Acinetobacter Sp. Adp1
Protocatechuate 3,4- Dioxygenase In Complex With
3,4-Dihydroxybenzoate
pdb|1EOC|B Chain B, Crystal Structure Of Acinetobacter Sp. Adp1
Protocatechuate 3,4- Dioxygenase In Complex With
4-Nitrocatechol
pdb|2BUM|B Chain B, Crystal Structure Of Wild-Type Protocatechuate 3,4-
Dioxygenase From Acinetobacter Sp. Adp1
pdb|2BUQ|B Chain B, Crystal Structure Of Wild-Type Protocatechuate 3,4-
Dioxygenase From Acinetobacter Sp. Adp1 In Complex With
Catechol
pdb|2BUR|B Chain B, Crystal Structure Of Wild-Type Protocatechuate 3,4-
Dioxygenase From Acinetobacter Sp. Adp1 In Complex With
4- Hydroxybenzoate
pdb|2BUX|B Chain B, Crystal Structure Of Protocatechuate 3,4-Dioxygenase From
Acinetobacter Sp. Adp1 Mutant R133h
pdb|2BUY|B Chain B, Crystal Structure Of Protocatechuate 3,4-Dioxygenase From
Acinetobacter Sp. Adp1 Mutant R133h In Complex With
Catechol
pdb|2BUZ|B Chain B, Crystal Structure Of Protocatechuate 3,4-Dioxygenase From
Acinetobacter Sp. Adp1 Mutant R133h In Complex With 4-
Nitrocatechol
pdb|2BV0|B Chain B, Crystal Structure Of Protocatechuate 3,4-Dioxygenase From
Acinetobacter Sp. Adp1 Mutant R133h In Complex With
Protocatechuate
Length = 241
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 39/100 (39%), Gaps = 14/100 (14%)
Query: 7 EAAFAKSHYPDIYCREELAILFQVWFQNRRAKYRKQEKQLQKALTPSVIPTCNGAMMRN- 65
E + D + R L +VW N +YR Q A+ P+ C G M+ +
Sbjct: 77 ERVIVHGYVRDQFGRPVKNALVEVWQANASGRYRHPNDQYIGAMDPN-FGGC-GRMLTDD 134
Query: 66 ----IYPTTSRGYQPYPHPNTINRQ-----HFVILVPGMS 96
++ T G PYP N IN HF ++ G +
Sbjct: 135 NGYYVFRTIKPG--PYPWRNRINEWRPAHIHFSLIADGWA 172
>pdb|2BUT|B Chain B, Crystal Structure Of Protocatechuate 3,4-Dioxygenase From
Acinetobacter Sp. Adp1 Mutant R457s - Apo
pdb|2BUV|B Chain B, Crystal Structure Of Protocatechuate 3,4-Dioxygenase From
Acinetobacter Sp. Adp1 Mutant R457s In Complex With
Protocatechuate
pdb|2BUU|B Chain B, Crystal Structure Of Protocatechuate 3,4-Dioxygenase From
Acinetobacter Sp. Adp1 Mutant R457s In Complex With 4-
Nitrocatechol
pdb|2BUW|B Chain B, Crystal Structure Of Protocatechuate 3,4-Dioxygenase From
Acinetobacter Sp. Adp1 Mutant R457s In Complex With 4-
Hydroxybenzoate
Length = 241
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 26/100 (26%), Positives = 39/100 (39%), Gaps = 14/100 (14%)
Query: 7 EAAFAKSHYPDIYCREELAILFQVWFQNRRAKYRKQEKQLQKALTPSVIPTCNGAMMRN- 65
E + D + R L +VW N +YR Q A+ P+ C G M+ +
Sbjct: 77 ERVIVHGYVRDQFGRPVKNALVEVWQANASGRYRHPNDQYIGAMDPN-FGGC-GRMLTDD 134
Query: 66 ----IYPTTSRGYQPYPHPNTINRQ-----HFVILVPGMS 96
++ T G PYP N IN HF ++ G +
Sbjct: 135 NGYYVFRTIKPG--PYPWRNRINEWSPAHIHFSLIADGWA 172
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 2 QLAELEAAFAKSHYPDIYCREELA-------ILFQVWFQNRRAKYRKQEKQLQKAL 50
Q+ ELE F+ Y R LA ++WFQNRR Y+ + KQL L
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR--YKTKRKQLSSEL 68
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 27.3 bits (59), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAIL-------FQVWFQNRRAKYRK 41
QL ELE +A + + R ++ +WFQNRR K +K
Sbjct: 18 QLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAIL-------FQVWFQNRRAKYRK 41
QL ELE +A + + R +++ +WFQNRR K +K
Sbjct: 18 QLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAIL-------FQVWFQNRRAKYRK 41
QL ELE +A + + R ++ +WFQNRR K +K
Sbjct: 12 QLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQEKQLQK 48
Q ELE F + Y R E+A L ++WFQNRR K +K K K
Sbjct: 24 QTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDRAK 77
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 27 LFQVWFQNRRAKYRK 41
+ QVWFQN RA+ RK
Sbjct: 60 VVQVWFQNTRARERK 74
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRKQ 42
Q ELE F + Y R E+A ++WFQNRR K++K+
Sbjct: 14 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRK 41
Q ELE F + Y RE LA L ++WFQN R K ++
Sbjct: 20 QTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 2 QLAELEAAFAKSHYPDIYCREELAILF-------QVWFQNRRAKYRK 41
Q ELE F + Y R E+A + ++WFQNRR K +K
Sbjct: 12 QTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>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 = 25.8 bits (55), Expect = 7.5, Method: Composition-based stats.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 29 QVWFQNRRAKYRKQ 42
++WFQNRR K++K+
Sbjct: 4 KIWFQNRRMKWKKR 17
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
0.319 0.130 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,806,138
Number of Sequences: 62578
Number of extensions: 127942
Number of successful extensions: 299
Number of sequences better than 100.0: 69
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 33
Number of HSP's that attempted gapping in prelim test: 251
Number of HSP's gapped (non-prelim): 69
length of query: 128
length of database: 14,973,337
effective HSP length: 87
effective length of query: 41
effective length of database: 9,529,051
effective search space: 390691091
effective search space used: 390691091
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)