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= 027468
(223 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.8 bits (107), Expect = 2e-05, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 34/54 (62%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQI 95
+++Q+ +L + + RP++ MK ++ + GL PR + +WFQNKR + K + I
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS EQ+ L+ F R + +++ ELGL Q+ IWFQNKRA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 40/59 (67%), Gaps = 4/59 (6%)
Query: 35 TGNNKRR----FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
+G++ RR F+DEQ+++LE +F+ P+ + ++A ++ L+ +V +WF+N+RA+
Sbjct: 3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 29/50 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS EQ+ L+ F R + +++ ELGL Q+ IWFQNKRA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 32/51 (62%)
Query: 41 RFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
RF+D Q++ L+ F++ A P+ ++++ L L R + +WFQN R +++
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
FS EQ+ L+ F R + +++ ELGL Q+ IWFQNKRA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 29/50 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS EQ+ L+ F R + +++ ELGL Q+ IWF+NKRA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 29/49 (59%)
Query: 41 RFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
RFS++Q LE FE++ + R+A L L RQV WFQN+RA+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 29/50 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS EQ+ L+ F R + +++ ELGL Q+ IWFQN+RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
+ EQ++ L + ++ P +M +A E+GL+ R V +WFQN RAR +
Sbjct: 24 ITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARER 73
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 28/50 (56%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS EQ+ L+ F R + +++ ELGL Q+ IWFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 31 ASFGTGNNKRR----FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNK 86
AS G N KR+ F+ Q LE F + + + +A + L P QV IWFQN
Sbjct: 1 ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60
Query: 87 RARSKTKQIEREY 99
R ++K Q E+ Y
Sbjct: 61 RYKTKRAQNEKGY 73
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 28/50 (56%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS EQ+ L+ F R + +++ ELGL Q+ IWF NKRA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 27/48 (56%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
FS EQ+ + F R + +++ ELGL Q+ IWFQNKRA+
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIEREY 99
F+ Q++ LE +F P + +A +L L+ ++ IWFQN+RA+ K E ++
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQF 65
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 32/52 (61%)
Query: 38 NKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
N+ F+ EQ+++LE FE P+ + R+A ++ L ++ +WF N+RA+
Sbjct: 10 NRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 61
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 9/88 (10%)
Query: 13 AVKFRGLNLDWTDMQQPIASF---GTGNNKRR------FSDEQVKSLEFMFESEARPESR 63
A K + + W + + + + G N+R+ S +LE F ++P S+
Sbjct: 56 ACKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQ 115
Query: 64 MKHRMADELGLQPRQVAIWFQNKRARSK 91
RMA+EL L+ V +WF N+R R K
Sbjct: 116 EIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 50 LEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
LE +F + S+ K +A + G+ P QV +WF NKR RSK
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 21/29 (72%)
Query: 63 RMKHRMADELGLQPRQVAIWFQNKRARSK 91
R + +++ ELGL Q+ IWFQNKRA+ K
Sbjct: 14 RRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 30 IASFGTGNNKRR----FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQN 85
+A GT +RR ++ Q LE F + R + MA L L RQ+ IWFQN
Sbjct: 11 MAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQN 70
Query: 86 KRARSK 91
+R + K
Sbjct: 71 RRMKLK 76
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 50 LEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
LE +F + S+ K +A + G+ P QV +WF NKR RSK
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1YRN|A Chain A, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1F43|A Chain A, Solution Structure Of The Mata1 Homeodomain
Length = 61
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 50 LEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
LE +F + S+ K +A + G+ P QV +WF NKR RSK
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%)
Query: 50 LEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
LE +F + S+ K +A + G+ P QV +WF NKR RSK
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 32/57 (56%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIERE 98
F Q+++++ F P+++ ++A + GL R + +WFQN RA+ + + +E
Sbjct: 14 FKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQE 70
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 4/70 (5%)
Query: 34 GTGNNKRR----FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
G N KR+ F+ Q LE F + + + + + L P QV IWFQN R +
Sbjct: 7 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYK 66
Query: 90 SKTKQIEREY 99
+K Q E+ Y
Sbjct: 67 TKRAQNEKGY 76
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 35.4 bits (80), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 35 TGNNKRR----FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARS 90
+G++ RR F+ Q+ LE +F P+ M+ +A ++ L +V +WF+N+RA+
Sbjct: 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKC 62
Query: 91 K 91
+
Sbjct: 63 R 63
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 35.0 bits (79), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 49 SLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
SLE MF +P + +A++LGL+ V +WF N+R + K
Sbjct: 110 SLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>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 = 35.0 bits (79), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
FS Q+ LE FE P+ + +A L ++ +WFQN+RAR
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRAR 72
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 35.0 bits (79), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 36 GNNKRR---FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
G ++RR F+ EQ+ LE F + + ++A L L QV IWFQN+RA+
Sbjct: 5 GKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 34.7 bits (78), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 31 ASFGTGNNKRR--FSDEQVKSLEFMFESE---ARPESRMKHRMADELGLQPRQVAIWFQN 85
S G+ K R +S Q+ +L+ F+ A PE + +A LGL QV IWFQN
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPE---RAELAASLGLTQTQVKIWFQN 57
Query: 86 KRARSK 91
KR++ K
Sbjct: 58 KRSKIK 63
>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 = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 28/50 (56%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS QV LE F+ + + + ++A L L QV IWFQN+R +SK
Sbjct: 9 FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 34.7 bits (78), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 28/53 (52%)
Query: 46 QVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIERE 98
QV LE F + + + +A L L QV IWFQN+R ++K KQ+ E
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 34.7 bits (78), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS EQ+ L+ F R + +++ ELGL QV WF+N RA+ K
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 34.3 bits (77), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 34 GTGNNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
G ++ F+ EQ++ LE FE P+ + +A L +V +WF N+RAR
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 34.3 bits (77), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 39 KRR--FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
KRR FS QV LE F+ + + + +A + L P QV IWFQN R + K
Sbjct: 4 KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 33.9 bits (76), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIE 96
F+D Q ++L +F+ RP ++ ++ +LGL+ V+ +F N R RS K +E
Sbjct: 104 FTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLE 158
>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 = 33.9 bits (76), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 68 MADELGLQPRQVAIWFQNKRARSK 91
+A+ L L RQ+ IWFQN+R +SK
Sbjct: 36 IANALSLSERQIKIWFQNRRMKSK 59
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 33.9 bits (76), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 49 SLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
SLE MF +P + +A++LGL+ V +WF N+R + K
Sbjct: 22 SLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 33.9 bits (76), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 28/48 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
F+ Q++ LE F P+ + +A ++GL ++ +WFQN+RA+
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 53
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 33.5 bits (75), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 28/48 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
F+ Q++ LE F P+ + +A ++GL ++ +WFQN+RA+
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 53
>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 = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 28/48 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
F+ Q++ LE F P+ + +A ++GL ++ +WFQN+RA+
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 60
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%)
Query: 38 NKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
N+ F+ Q++ LE +F+ P+ + ++A L +V +WFQN+RA+
Sbjct: 12 NRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
++ Q+K LE + + + R++ L RQV IWFQN+R + K
Sbjct: 8 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
++ Q+K LE + + + R++ L RQV IWFQN+R + K
Sbjct: 14 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRAR 89
F++ Q+ LE FE + + + +A+ LGL QV W+QN+R +
Sbjct: 24 FTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 31 ASFGTGNNKRR--FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRA 88
S G+ K+R +S Q++ LE + + + +++ L RQ+ IWFQN+R
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV 60
Query: 89 RSK 91
+ K
Sbjct: 61 KEK 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 31.6 bits (70), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 51 EFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
EF+F + R + +A L L RQV IWFQN+R + K
Sbjct: 31 EFLFNMYLTRDRR--YEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQ 94
F+ +Q++ LE F+ P+ + +A L +V +WF+N+RA+ + ++
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 30.4 bits (67), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
F+ Q+ +LE F + + + L L QV IWFQN+RA++K
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>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 = 30.4 bits (67), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQ 94
F+ +Q++ LE F+ P+ + +A L +V +WF+N+RA+ + ++
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 30.4 bits (67), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 27/46 (58%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKR 87
F+D Q ++L +F+ RP ++ ++ +LGL+ V+ +F N R
Sbjct: 102 FTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 147
>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 = 30.4 bits (67), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
++ Q LE F R + +A L L RQ+ IWFQN+R + K
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 30.4 bits (67), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 26/50 (52%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
FS Q+ L F+ + + +++ L L +QV WFQN+R +SK
Sbjct: 29 FSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>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 = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
++ Q LE F R + +A L L RQ+ IWFQN+R + K
Sbjct: 35 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 41 RFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQN 85
R +D+Q++ L F+ P MAD+ GL + + WF+N
Sbjct: 13 RITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 39 KRRFSDEQVKSL--EFMFE--SEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
KRR ++Q + E+ + S P K +A + G+ QV+ WF NKR R K
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 60 PESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQI-ERE 98
P R K +A+ GL QV+ WF+N+R R + + ERE
Sbjct: 519 PSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERE 558
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 68 MADELGLQPRQVAIWFQNKRARSK 91
+A L L RQ+ IWFQN+R + K
Sbjct: 36 IAHALSLTERQIKIWFQNRRMKWK 59
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 30 IASFGTGNNKRRFSDEQVK-SLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRA 88
IA+ G KR + VK +LE F +P + +AD L L+ V +WF N+R
Sbjct: 93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQ 152
Query: 89 RSK 91
+ K
Sbjct: 153 KEK 155
>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 = 29.6 bits (65), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
++ Q LE F R + +A L L RQ+ IWFQN+R + K
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>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 = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
++ Q LE F R + +A L L RQ+ IWFQN+R + K
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 58
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 18/36 (50%)
Query: 56 SEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
S P K +A + G+ QV+ WF NKR R K
Sbjct: 27 SNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|4A4A|A Chain A, Cpgh89 (E483q, E601q), From Clostridium Perfringens, In
Complex With Its Substrate Glcnac-Alpha-1,4-Galactose
Length = 914
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 179 STVIMKDFAATNVEEQTESSGNWCKFE 205
S ++ +DF N E QT S G WC F+
Sbjct: 409 SGMVPRDFKEKNQEAQTISQGGWCGFD 435
>pdb|2VC9|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With 2-Acetamido-1,2-Dideoxynojirmycin
pdb|2VCA|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With Beta-N-Acetyl-D-Glucosamine
pdb|2VCB|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
In Complex With Pugnac
pdb|2VCC|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
Length = 891
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 179 STVIMKDFAATNVEEQTESSGNWCKFE 205
S ++ +DF N E QT S G WC F+
Sbjct: 386 SGMVPRDFKEKNQEAQTISQGGWCGFD 412
>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 = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 36 GNNKRR---FSDEQVKSLE--FMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARS 90
G+NKR ++ Q+ LE F+F R++ +A L L R + IWFQN+R +
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVE--LAVMLNLTERHIKIWFQNRRMKW 58
Query: 91 K 91
K
Sbjct: 59 K 59
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 39 KRRFSDEQVKSL--EFMFE--SEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
KRR ++Q + E+ + S P K +A + G+ QV+ WF NKR R K
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 39 KRRFSDEQVKSL-EFMFE--SEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
+R FS + + L E+ + S P K +A + G+ QV+ WF NKR R K
Sbjct: 5 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIE 96
F+ Q+ LE F + +A L L QV IWFQN+R + K ++ E
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.5 bits (62), Expect = 3.0, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 51 EFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
EF+F + R + +A L L RQV IWFQN+R + K
Sbjct: 19 EFLFNMYLTRDRR--YEVARVLNLTERQVKIWFQNRRMKMK 57
>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 = 28.5 bits (62), Expect = 3.0, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 27/53 (50%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQ 94
FS Q+ +L+ F+ + + ++ L L +QV WFQN+R + K Q
Sbjct: 10 FSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>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 = 3.6, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 67 RMAD---ELGLQPRQVAIWFQNKRARSKTK 93
R+AD +L L QV IWF+N+R R K +
Sbjct: 31 RLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 39 KRRFSDEQVKSL--EFMFE--SEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
KRR ++Q + E+ + S P K +A + G+ QV+ WF NKR R K
Sbjct: 5 KRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 49 SLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
+LE F +P S +AD+L ++ + +WF N+R + K
Sbjct: 114 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 22/46 (47%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKR 87
FS QV LE F + S + +A L + QV WFQN+R
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 49 SLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
+LE F +P S +AD+L ++ + +WF N+R + K
Sbjct: 117 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 49 SLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
+LE F +P S +AD+L ++ + +WF N+R + K
Sbjct: 118 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 49 SLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
+LE F +P S +AD+L ++ + +WF N+R + K
Sbjct: 110 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 152
>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 = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
F+ +Q+ LE F E + +A +L L + +WFQN+R + K
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 49 SLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
+LE F +P S +AD+L ++ + +WF N+R + K
Sbjct: 21 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 27 QQPIASFGTG----NNKRR--FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVA 80
QQ + F G KRR F+ + +++L FE P + A EL V
Sbjct: 79 QQNLXEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVR 138
Query: 81 IWFQNKR 87
+WF N+R
Sbjct: 139 VWFSNRR 145
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And
Homeoboxes Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And
Homeoboxes Protein 2, Homeodomain 2)
Length = 66
Score = 26.9 bits (58), Expect = 8.6, Method: Composition-based stats.
Identities = 13/52 (25%), Positives = 25/52 (48%)
Query: 40 RRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
R+ + EQ+ L+ F P+ +R+ + GL ++ WF + R R +
Sbjct: 9 RKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQ 60
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
0.310 0.124 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,720,865
Number of Sequences: 62578
Number of extensions: 191393
Number of successful extensions: 378
Number of sequences better than 100.0: 87
Number of HSP's better than 100.0 without gapping: 85
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 293
Number of HSP's gapped (non-prelim): 87
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 49 (23.5 bits)