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= 046202
(448 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q+ L+ F + + E +R+QLS ELGL+ QIK WFQNKR + K
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q+ L+ F + + E +R+QLS ELGL+ QIK WFQNKR + K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 31/47 (65%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQ 70
++ Q+ L+ F + + E +R+QLS ELGL+ QIK WFQNKR +
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 32/49 (65%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q+ L+ F + + E +R+QLS ELGL+ QIK WFQN+R + K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 9/79 (11%)
Query: 9 ATNSQNKGKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKR 68
++ S K T +H HQ++T++++F +PD +QL+++ GL + ++ WFQN R
Sbjct: 2 SSGSSGKRMRTSFKH--HQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNAR 59
Query: 69 TQTKAQNERANNSVLRAEN 87
+ + ++LR EN
Sbjct: 60 AKFR-------RNLLRQEN 71
>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 = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 32/49 (65%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q+ L+ F + + E +R+QLS ELGL+ QIK WF+NKR + K
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>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 = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q+ L+ F + + E +R+QLS ELGL+ QIK WF NKR + K
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q+ L+ F + + E +R+QLS ELGL+ QIK WFQN R + K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 32/53 (60%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
T+ Q++ LE F +PD R +L+ ++GL +I+ WFQN+R + + Q +
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q+ + F + + E +R+QLS ELGL+ QIK WFQNKR + +
Sbjct: 11 SSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 31/51 (60%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQ 74
T+ Q++ LE F +PD R +L+ ++GL +I+ WFQN+R + + Q
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 32/53 (60%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
T+ Q++ LE F +PD R +L+ ++GL +I+ WFQN+R + + Q +
Sbjct: 14 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 20/38 (52%), Positives = 26/38 (68%)
Query: 35 FKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
F + + E +R+QLS ELGL+ QIK WFQNKR + K
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 31/47 (65%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQ 70
T Q++ LE F++ +PD R QL++++ L ++++ WF+N+R +
Sbjct: 15 TDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 29/51 (56%)
Query: 22 RHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
R T +Q++ L+ FF +P +++ QLS L L + I WFQN R + +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 10 TNSQNKGKITCHR--HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNK 67
++ NKGK +R T++Q++ LE F+ +PD R QL+ L +++ WFQN+
Sbjct: 1 SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 68 RTQ 70
R +
Sbjct: 61 RAK 63
>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 = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 31/49 (63%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q+ L+ F + + E +R+QLS ELGL+ Q+K WF+N R + K
Sbjct: 12 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 30/50 (60%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
+++ Q+ L+ F+ + +R +L+ LGL Q+K WFQNKR++ K
Sbjct: 14 YSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>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 = 38.5 bits (88), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 27 QIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQN 75
Q+ TL + P PD + QL + GL + I+ WFQNKR + K ++
Sbjct: 14 QLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62
>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 = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 32/53 (60%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
T+ Q+Q LEA F+ +PD + R +++ L +++ WF+N+R + + + E
Sbjct: 11 TSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 37.7 bits (86), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
T +QI+ LE F+ +P + L+++L L+L +I+ WFQN+R + K
Sbjct: 9 TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLK 57
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNERANN 80
T Q+ LEA F +PD R +++ ++ L +++ WF+N+R + + Q ++ N
Sbjct: 15 TRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQN 71
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
TT Q+ LE F+ + +R + S L L Q+K WFQN+R + K
Sbjct: 8 TTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 36.2 bits (82), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 20 CHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKA--QNER 77
C + + + L ++ P+P ++R+L++ GL Q+ WF+N+R + +A ER
Sbjct: 500 CFKEKSRGV--LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKER 557
Query: 78 AN 79
N
Sbjct: 558 EN 559
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 36.2 bits (82), Expect = 0.041, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 31/54 (57%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
+T HQ LE F + ++R ++++ L L +Q+K WFQN+R + K N+
Sbjct: 20 YTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 22 RHTTHQIQTL--EAFFKDC--PHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
RH Q + E F+ P+P E + +L+K+ G+ + Q+ WF NKR + K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 32/53 (60%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
T+ Q+Q LEA F+ +PD + R +++ L +++ WF+N+R + + + E
Sbjct: 11 TSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 35.8 bits (81), Expect = 0.048, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 39 PHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
P+P E + +L+K+ G+ + Q+ WF NKR + K
Sbjct: 27 PYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 35.8 bits (81), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 32 EAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
+ F HPDE + LSK+L D++ I+ WF+ +R Q K
Sbjct: 17 KVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>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 = 35.8 bits (81), Expect = 0.055, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 27 QIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
Q+ LE FK + +R QL+ L L Q+K WFQN+R ++K
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 35.8 bits (81), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 30 TLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
+LE F CP P Q ++ +LGL+ ++ WF N+R + K
Sbjct: 22 SLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 35.4 bits (80), Expect = 0.059, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNERAN 79
T QI+ LE F+ +PD R +L+ ++ L +I+ WF N+R + + + + N
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN 70
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
Length = 67
Score = 35.4 bits (80), Expect = 0.061, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 39 PHPDENQRRQLSKELGLDLKQIKFWFQNKR 68
P+P E Q++QL+++ GL + Q+ WF N R
Sbjct: 24 PYPSEEQKKQLAQDTGLTILQVNNWFINAR 53
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 35.4 bits (80), Expect = 0.066, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 39 PHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
P+P E + +L+K+ G+ + Q+ WF NKR + K
Sbjct: 28 PYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 35.4 bits (80), Expect = 0.069, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 39 PHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
P+P E + +L+K+ G+ + Q+ WF NKR + K
Sbjct: 27 PYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>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 = 35.0 bits (79), Expect = 0.074, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK-AQNERA 78
T Q LE F+ + +R L+ + L Q+K WFQN R +TK AQNE+
Sbjct: 17 TKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKG 72
>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 = 35.0 bits (79), Expect = 0.081, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
+T +Q LE F + +R +++ L L +QIK WFQN+R + K +N+
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>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 = 35.0 bits (79), Expect = 0.089, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
+T +Q LE F + +R +++ L L +QIK WFQN+R + K +N+
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 35.0 bits (79), Expect = 0.092, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 30/53 (56%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQN 75
+T +Q LE F + ++R ++++ L L +Q+K WFQN+R + K N
Sbjct: 8 YTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60
>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 = 35.0 bits (79), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKR 68
T I+ L A+F+ P P + + +KEL D + ++ WF N+R
Sbjct: 101 TPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
>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 = 34.7 bits (78), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 29/52 (55%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQN 75
+ Q+ LE F+ +PD R +L++ L +I+ WFQN+R + + Q+
Sbjct: 26 SASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 29/54 (53%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNER 77
T+ QI LE F + + LS +L L Q+K WF+N+R + K Q+++
Sbjct: 10 TSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 28/52 (53%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQ 74
+T +Q LE F + +R +++ L L +QIK WFQN+R + K +
Sbjct: 27 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 28/51 (54%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQ 74
T Q++ LE F+ +PD R +L++ L +++ WF N+R + + Q
Sbjct: 10 TAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 11 NSQNKGKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQN 66
+S + GK R T Q++ L +F P E Q ++++ + GL K IK WF+N
Sbjct: 2 SSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 29/53 (54%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQN 75
+T +Q LE F + +R +++ L L +QIK WFQN+R + K +N
Sbjct: 10 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQ 74
TT Q+ LE F + +R +++ L L+ Q+K WFQN+R + K +
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 92
>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 = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 39 PHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
P+P E + +L+++ G+ + Q+ WF NKR + K
Sbjct: 27 PYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>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 = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
+T +Q LE F + +R +++ L L +QIK WFQN+R + K +N+
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
>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 = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%)
Query: 27 QIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
Q+ LE F + +R L+K L L Q+K WFQN+R +TK
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTK 60
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 28/50 (56%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
++ Q++ LE + +++RR++S L +QI WFQN+R + K
Sbjct: 14 YSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 30 TLEAFFKDC-PHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
TLE F +PDE + + LSK+L +++I+ WF+++R Q K
Sbjct: 22 TLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
>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 = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNERANNSVL 83
T Q+ LE F + +R L++ L + Q+K WFQN+RT+ + Q +
Sbjct: 25 TRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAER 84
Query: 84 RAEN 87
+A N
Sbjct: 85 QAAN 88
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 28/50 (56%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
+T Q++ LE + +++RR++S L +Q+ WFQN+R + K
Sbjct: 8 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>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 = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 3 LGDEQDATNSQNKGKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKF 62
LG N + K + T + T +Q LE F + +R +++ L L +QIK
Sbjct: 17 LGTSTVNANGETKRQRTSY--TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 74
Query: 63 WFQNKRTQTKAQNE 76
WFQN+R + K +++
Sbjct: 75 WFQNRRMKWKKEHK 88
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK-AQNERA 78
T Q LE F+ + +R L+ + L Q+K WFQN R +TK AQNE+
Sbjct: 20 TKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQNEKG 75
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 33.1 bits (74), Expect = 0.30, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 26/49 (53%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
T+ Q+ LE F + +R Q++ L L Q+K WFQN+R + K
Sbjct: 15 TSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 33.1 bits (74), Expect = 0.31, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 28/50 (56%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
+T Q++ LE + +++RR++S L +Q+ WFQN+R + K
Sbjct: 14 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 30 TLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
+LE F P P Q ++ +LGL+ ++ WF N+R + K
Sbjct: 110 SLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 15 KGKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
KG+ + T Q+ LE F+ + R L++ LGL Q+K W+QN+R + K
Sbjct: 16 KGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>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 = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%)
Query: 16 GKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
K T +T +Q LE F + +R ++ L L +QIK WFQN+R ++K
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 32.3 bits (72), Expect = 0.52, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 24/48 (50%)
Query: 27 QIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQ 74
Q+ LE FK + +R L+ + L Q+K WFQN R + K Q
Sbjct: 13 QVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 22 RHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQ 70
R + Q LE F+ + +R++L+K L L +Q+K WFQN+R +
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 27 QIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQ 74
Q+ LE F + +R L+K L + Q+K WFQN+RT+ + Q
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 32.0 bits (71), Expect = 0.66, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 27 QIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
Q+ L+ F+ + Q ++LS L L KQ+K WFQN+R + K
Sbjct: 14 QLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>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 = 32.0 bits (71), Expect = 0.79, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 24 TTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQ 74
T Q+ LE F + +R +L+ +L L IK WFQN+R + K Q
Sbjct: 9 TRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 30 TLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
LE+ F CP P ++ L+ L L+ + ++ WF N+R + K
Sbjct: 113 ALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 21 HRHTTHQIQTLEAFFK---DCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
HR T ++ LE++F + P+ D L K L QIK W N+R + K
Sbjct: 7 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 61
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 39 PHPDENQRRQLSKELGLDLKQIKFWFQNKR 68
P+P E++++Q++ + L L Q+ WF N R
Sbjct: 33 PYPTEDEKKQIAAQTNLTLLQVNNWFINAR 62
>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 = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 3/65 (4%)
Query: 7 QDATNSQNKGKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQN 66
+D N+ K ++ T Q +TL A FK+ P + + +S++LGL+L + +F N
Sbjct: 91 KDRGNTPKKPRLV---FTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN 147
Query: 67 KRTQT 71
R ++
Sbjct: 148 ARRRS 152
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 21 HRHTTHQIQTLEAFFK---DCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKA 73
HR T ++ LE++F + P+ D L K L QIK W N+R + K
Sbjct: 3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 15/67 (22%), Positives = 30/67 (44%)
Query: 11 NSQNKGKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQ 70
+S + G Q++ LE+ F P P + + +L E + ++I WF +R +
Sbjct: 2 SSGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61
Query: 71 TKAQNER 77
A+ +
Sbjct: 62 VNAEETK 68
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 7 QDATNSQNKGKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQN 66
+D N+ K ++ T Q +TL A FK+ P + + +S++LGL+L + +F N
Sbjct: 89 KDRGNTPKKPRLV---FTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN 145
Query: 67 KR 68
R
Sbjct: 146 AR 147
>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 = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 22 RHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKR 68
+ T QI L+A F PD+ + +L + GL +IK WF + R
Sbjct: 10 KKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHR 56
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 30.4 bits (67), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 21 HRHTTHQIQTLEAFFK---DCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKA 73
HR T ++ LE++F + P+ D L K L QIK W N+R + K
Sbjct: 32 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 87
>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 = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 28/54 (51%)
Query: 23 HTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTKAQNE 76
+T Q+ LE F + +R +L+ L L + IK WFQN+R + K + +
Sbjct: 10 YTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEED 63
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
Length = 96
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 9 ATNSQNKGKITCHRHTTHQIQTLEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKR 68
A S + GKI + T Q+ L++ F P + +L+KE GL I WF + R
Sbjct: 20 APKSGSTGKIC--KKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTR 77
Query: 69 TQTKAQN 75
K N
Sbjct: 78 YAWKNGN 84
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 30.0 bits (66), Expect = 2.9, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 1 GDLGDEQDATNSQNKGKITCHRHTTHQI---QTLEAFFKDCPHPDENQRRQLSKELGLDL 57
G L +E+ N + + R TT I LE F + P + ++++EL L+
Sbjct: 74 GALYNEKVGANERKR-----KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEK 128
Query: 58 KQIKFWFQNKRTQTK 72
+ ++ WF N+R + K
Sbjct: 129 EVVRVWFCNRRQREK 143
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 45 QRRQLSKELGLDLKQIKFWFQNKRTQTK 72
Q ++LS L L KQ+K WFQN+R ++K
Sbjct: 51 QMQELSNILNLSYKQVKTWFQNQRMKSK 78
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 29.3 bits (64), Expect = 4.3, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 25/42 (59%)
Query: 31 LEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
LE F+ + ++ +++K+ G+ Q++ WF NKR ++K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 29.3 bits (64), Expect = 4.6, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 25/42 (59%)
Query: 31 LEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
LE F+ + ++ +++K+ G+ Q++ WF NKR ++K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 29.3 bits (64), Expect = 4.6, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 25/42 (59%)
Query: 31 LEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
LE F+ + ++ +++K+ G+ Q++ WF NKR ++K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|4HNV|A Chain A, Crystal Structure Of R54e Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNV|B Chain B, Crystal Structure Of R54e Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNV|C Chain C, Crystal Structure Of R54e Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNV|D Chain D, Crystal Structure Of R54e Mutant Of S. Aureus Pyruvate
Carboxylase
Length = 1173
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 232 PPSSTNIERYVIHPESYEKVFPRANHFKTSSARVESSKYSGMVTMNGMQLVEMLLDSDKW 291
P + +I YV++P+ YE+ N + S + + GM NG + VE+ +D K
Sbjct: 992 PVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGM--RNG-ETVEIEIDKGK- 1047
Query: 292 VDLFPTIVSKARTIQVLEPGINGNRN 317
++ K TI EP NGNR
Sbjct: 1048 -----RLIIKLETIS--EPDENGNRT 1066
>pdb|3HBL|A Chain A, Crystal Structure Of S. Aureus Pyruvate Carboxylase T908a
Mutant
pdb|3HBL|B Chain B, Crystal Structure Of S. Aureus Pyruvate Carboxylase T908a
Mutant
pdb|3HBL|C Chain C, Crystal Structure Of S. Aureus Pyruvate Carboxylase T908a
Mutant
pdb|3HBL|D Chain D, Crystal Structure Of S. Aureus Pyruvate Carboxylase T908a
Mutant
Length = 1150
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 11/85 (12%)
Query: 232 PPSSTNIERYVIHPESYEKVFPRANHFKTSSARVESSKYSGMVTMNGMQLVEMLLDSDKW 291
P + +I YV++P+ YE+ N + S + + GM NG + VE+ +D K
Sbjct: 969 PVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGM--RNG-ETVEIEIDKGK- 1024
Query: 292 VDLFPTIVSKARTIQVLEPGINGNR 316
++ K TI EP NGNR
Sbjct: 1025 -----RLIIKLETIS--EPDENGNR 1042
>pdb|3HB9|A Chain A, Crystal Structure Of S. Aureus Pyruvate Carboxylase A610t
Mutant
pdb|3HB9|B Chain B, Crystal Structure Of S. Aureus Pyruvate Carboxylase A610t
Mutant
pdb|3HB9|C Chain C, Crystal Structure Of S. Aureus Pyruvate Carboxylase A610t
Mutant
pdb|3HB9|D Chain D, Crystal Structure Of S. Aureus Pyruvate Carboxylase A610t
Mutant
Length = 1150
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 11/85 (12%)
Query: 232 PPSSTNIERYVIHPESYEKVFPRANHFKTSSARVESSKYSGMVTMNGMQLVEMLLDSDKW 291
P + +I YV++P+ YE+ N + S + + GM NG + VE+ +D K
Sbjct: 969 PVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGM--RNG-ETVEIEIDKGK- 1024
Query: 292 VDLFPTIVSKARTIQVLEPGINGNR 316
++ K TI EP NGNR
Sbjct: 1025 -----RLIIKLETIS--EPDENGNR 1042
>pdb|3HO8|A Chain A, Crystal Structure Of S. Aureus Pyruvate Carboxylase In
Complex With Coenzyme A
pdb|3HO8|D Chain D, Crystal Structure Of S. Aureus Pyruvate Carboxylase In
Complex With Coenzyme A
pdb|3HO8|C Chain C, Crystal Structure Of S. Aureus Pyruvate Carboxylase In
Complex With Coenzyme A
pdb|3HO8|B Chain B, Crystal Structure Of S. Aureus Pyruvate Carboxylase In
Complex With Coenzyme A
Length = 1150
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 11/85 (12%)
Query: 232 PPSSTNIERYVIHPESYEKVFPRANHFKTSSARVESSKYSGMVTMNGMQLVEMLLDSDKW 291
P + +I YV++P+ YE+ N + S + + GM NG + VE+ +D K
Sbjct: 969 PVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGM--RNG-ETVEIEIDKGK- 1024
Query: 292 VDLFPTIVSKARTIQVLEPGINGNR 316
++ K TI EP NGNR
Sbjct: 1025 -----RLIIKLETIS--EPDENGNR 1042
>pdb|4HNU|A Chain A, Crystal Structure Of K442e Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNU|B Chain B, Crystal Structure Of K442e Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNU|C Chain C, Crystal Structure Of K442e Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNU|D Chain D, Crystal Structure Of K442e Mutant Of S. Aureus Pyruvate
Carboxylase
Length = 1173
Score = 29.3 bits (64), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 232 PPSSTNIERYVIHPESYEKVFPRANHFKTSSARVESSKYSGMVTMNGMQLVEMLLDSDKW 291
P + +I YV++P+ YE+ N + S + + GM NG + VE+ +D K
Sbjct: 992 PVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGM--RNG-ETVEIEIDKGK- 1047
Query: 292 VDLFPTIVSKARTIQVLEPGINGNRN 317
++ K TI EP NGNR
Sbjct: 1048 -----RLIIKLETIS--EPDENGNRT 1066
>pdb|3BG5|A Chain A, Crystal Structure Of Staphylococcus Aureus Pyruvate
Carboxylase
pdb|3BG5|B Chain B, Crystal Structure Of Staphylococcus Aureus Pyruvate
Carboxylase
pdb|3BG5|C Chain C, Crystal Structure Of Staphylococcus Aureus Pyruvate
Carboxylase
pdb|3BG5|D Chain D, Crystal Structure Of Staphylococcus Aureus Pyruvate
Carboxylase
Length = 1173
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 232 PPSSTNIERYVIHPESYEKVFPRANHFKTSSARVESSKYSGMVTMNGMQLVEMLLDSDKW 291
P + +I YV++P+ YE+ N + S + + GM NG + VE+ +D K
Sbjct: 992 PVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGM--RNG-ETVEIEIDKGK- 1047
Query: 292 VDLFPTIVSKARTIQVLEPGINGNRN 317
++ K TI EP NGNR
Sbjct: 1048 -----RLIIKLETIS--EPDENGNRT 1066
>pdb|4HNT|A Chain A, Crystal Structure Of F403a Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNT|B Chain B, Crystal Structure Of F403a Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNT|C Chain C, Crystal Structure Of F403a Mutant Of S. Aureus Pyruvate
Carboxylase
pdb|4HNT|D Chain D, Crystal Structure Of F403a Mutant Of S. Aureus Pyruvate
Carboxylase
Length = 1173
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 232 PPSSTNIERYVIHPESYEKVFPRANHFKTSSARVESSKYSGMVTMNGMQLVEMLLDSDKW 291
P + +I YV++P+ YE+ N + S + + GM NG + VE+ +D K
Sbjct: 992 PVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGM--RNG-ETVEIEIDKGK- 1047
Query: 292 VDLFPTIVSKARTIQVLEPGINGNRN 317
++ K TI EP NGNR
Sbjct: 1048 -----RLIIKLETIS--EPDENGNRT 1066
>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 = 28.5 bits (62), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 25/42 (59%)
Query: 31 LEAFFKDCPHPDENQRRQLSKELGLDLKQIKFWFQNKRTQTK 72
LE F+ + ++ +++K+ G+ Q++ WF NKR ++K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.133 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,183,641
Number of Sequences: 62578
Number of extensions: 522933
Number of successful extensions: 1316
Number of sequences better than 100.0: 91
Number of HSP's better than 100.0 without gapping: 80
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1229
Number of HSP's gapped (non-prelim): 98
length of query: 448
length of database: 14,973,337
effective HSP length: 102
effective length of query: 346
effective length of database: 8,590,381
effective search space: 2972271826
effective search space used: 2972271826
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)