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= 026325
(240 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 50.8 bits (120), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 35/56 (62%)
Query: 86 PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
P+ K +S + LEE FR +LN K+KEE+A + + P QV VWF N+R RSK
Sbjct: 6 PKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 82 DGGPPRKKLR---LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138
DG P +K+ R +K Q+ LE FR L+ ++E LA+ ++L P QV++WFQN R
Sbjct: 3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY 62
Query: 139 RSKLKQTEMECE 150
++K Q E E
Sbjct: 63 KTKRAQNEKGYE 74
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 32/50 (64%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
+S + LE+ FR +LN K+KEE+A + + P QV VWF N+R RSK
Sbjct: 372 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 35/56 (62%)
Query: 86 PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
P+ K +S + LE+ FR +LN K+KEE+A + + P QV VWF N+R RSK
Sbjct: 6 PKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 39/65 (60%)
Query: 77 SCINVDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136
S +N +G R++ ++ Q+ LE+ F N L +++ E+A L L RQ+++WFQNR
Sbjct: 20 STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 79
Query: 137 RARSK 141
R + K
Sbjct: 80 RMKWK 84
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 48.9 bits (115), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 82 DGGPPRKKLR---LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138
DG P +K+ R +K Q+ LE FR L+ ++E L + ++L P QV++WFQN R
Sbjct: 6 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRY 65
Query: 139 RSKLKQTEMECE 150
++K Q E E
Sbjct: 66 KTKRAQNEKGYE 77
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/43 (51%), Positives = 29/43 (67%)
Query: 99 LLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
LE+ FR +LN K+KEE+A + + P QV VWF N+R RSK
Sbjct: 11 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 34/51 (66%)
Query: 89 KLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139
++R S +Q+ LE+ F L+P +++ LA L+L RQV+ WFQNRRA+
Sbjct: 11 QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 45.1 bits (105), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 37/65 (56%)
Query: 77 SCINVDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136
+ +G R + ++ Q+ LE+ F NH L +++ E+A L L RQ+++WFQNR
Sbjct: 12 AIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNR 71
Query: 137 RARSK 141
R + K
Sbjct: 72 RMKLK 76
>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 = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 29/50 (58%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTEMEC 149
LE F H L+ ++ LA LKL QV++WFQNRR ++K KQ E
Sbjct: 19 LERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSEL 68
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
S+ Q LE F+ L+ ++++LA+ LKL QV++WFQNRR +SK
Sbjct: 9 FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 42.4 bits (98), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 2/66 (3%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQTE 146
R + ++ Q +LE FR N E+LA +L L+ ++++WFQNRRA KLK++
Sbjct: 3 RPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRA--KLKRSH 60
Query: 147 MECEYL 152
E ++L
Sbjct: 61 RESQFL 66
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 42.4 bits (98), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
+K+ +K Q+ LE+ F N L ++ E+A L L RQV++WFQNRR + K
Sbjct: 15 KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 30/46 (65%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQT 145
LE+ F N + +++ ++A L L RQ+++WFQNRR +SK +T
Sbjct: 18 LEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRT 63
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 27/42 (64%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
LE FR L+ ++ E ++ L L QV++WFQNRRA++K
Sbjct: 15 LERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 42.0 bits (97), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
+K+ +K Q+ LE+ F N L ++ E+A L L RQV++WFQNRR + K
Sbjct: 3 KKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 32/58 (55%)
Query: 84 GPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
G R + + EQ LE +F H + +EELA + KL +V+VWF NRRAR +
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWR 58
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 35/64 (54%)
Query: 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142
G P + + Q LE+ F N L+ ++ E+A L+L QV++WFQNRR + K
Sbjct: 32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
Query: 143 KQTE 146
++ E
Sbjct: 92 RERE 95
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 41.2 bits (95), Expect = 5e-04, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 33/55 (60%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
++++ S+ Q LE F+ L+ ++E LA+ + L P QV++WFQN R + K
Sbjct: 4 KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 34/59 (57%)
Query: 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
G R++ + +Q + LE +F+ NH + +EE+A L +V VWF+NRRA+ +
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWR 59
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 34/59 (57%)
Query: 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
G R++ + EQ LE+ F L+ ++ ++A LKL QV++WFQNRRA+ K
Sbjct: 5 GKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 40.8 bits (94), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
R + ++ Q+ LE+ F N L +++ E+A L L RQ+++WFQNRR + K
Sbjct: 5 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>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 = 40.4 bits (93), Expect = 8e-04, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 31/49 (63%)
Query: 93 SKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
++ Q+ LE+ F N L +++ E+A L L RQ+++WFQNRR + K
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>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 = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
S EQ L+ F N L +++++L+++L L Q+++WFQN+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 40.4 bits (93), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 94 KEQSR-LLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
KE+SR +L E + HN +P++K ELA L QV WF+NRR R +
Sbjct: 502 KEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 550
>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 = 40.4 bits (93), Expect = 9e-04, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
R + ++ Q+ LE+ F N L +++ E+A L L RQ+++WFQNRR + K
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
S EQ L+ F N L +++++L+++L L Q+++WFQN+RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>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 = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
R + ++ Q+ LE+ F N L +++ E+A L L RQ+++WFQNRR + K
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 58
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 31/48 (64%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139
S EQ L+ F N L +++++L+++L L Q+++WFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 31/55 (56%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
+K++ SK Q R LE + N + ++ +++ L RQ+ +WFQNRR + K
Sbjct: 9 KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQT 145
S EQ L+ F N L +++++L+++L L Q+++WFQN AR+K+K++
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQN--ARAKIKKS 59
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
S EQ L+ F N L +++++L+++L L Q+++WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 84 GPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLK 143
GP R + + Q LE+ F L + +L+ +L L QV++WF+NRR R K++
Sbjct: 1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 32/50 (64%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
S EQ L+ F N L +++++L+++L L Q+++WF+N+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
G R + ++ Q LE+ F N ++ ++ ELA L L R +++WFQNRR + K
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 59
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139
G R + S EQ + F N L +++++L+++L L Q+++WFQN+RA+
Sbjct: 1 GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 28/42 (66%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
LE++F H + +EELA ++ L +++VWFQNRRA+ +
Sbjct: 14 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 37/76 (48%)
Query: 72 DDEEESCINVDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEV 131
D E E I + R + S Q LE +F + +EELA + L +++V
Sbjct: 5 DCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV 64
Query: 132 WFQNRRARSKLKQTEM 147
WFQNRRAR + + T +
Sbjct: 65 WFQNRRARLRKQHTSV 80
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
S EQ L+ F N L +++++L+++L L Q+++WF N+RA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|2ECB|A Chain A, The Solution Structure Of The Third Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein
Length = 89
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 84 GP---PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARS 140
GP P+K + EQ R+L+ SF ++ L ++ L Q KL R+++ WF ++
Sbjct: 7 GPDFTPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSK 66
Query: 141 KLKQTEMECE 150
LK+ +ME +
Sbjct: 67 ALKEEKMEID 76
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 28/42 (66%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
LE++F H + +EELA ++ L +++VWFQNRRA+ +
Sbjct: 14 LEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 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 = 37.7 bits (86), Expect = 0.006, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 87 RKKLRLSKEQSRL--LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKLKQ 144
++K+R Q++L L++ F+ L+ +Q +EL++ L L +QV+ WFQN+R + K Q
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>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 = 37.7 bits (86), Expect = 0.006, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNP----KQKEELATQLKLKPRQVEVWFQNRRARSK 141
RK+ SK+ S +L E F ++H NP + KEELA + + QV WF N+R R K
Sbjct: 3 RKRRNFSKQASEILNEYF-YSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 84 GPPRKKLR----LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139
P RK+ R + Q LE++F H + +EELA ++ L +++VWFQNRRA+
Sbjct: 1 APKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 60
Query: 140 SK 141
+
Sbjct: 61 WR 62
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNP----KQKEELATQLKLKPRQVEVWFQNRRARSK 141
RK+ +K+ + +L E F ++H NP + KEELA + + QV WF N+R R K
Sbjct: 3 RKRRNFNKQATEILNEYF-YSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>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 = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 83 GGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
G R++ + +Q + LE +F+ N + +EE+A L +V VWF+NRRA+ +
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWR 59
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 84 GPPRKKLRLS--KEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139
G K++R S Q R ++ F NH + K ++LA + L R ++VWFQN RA+
Sbjct: 4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 28/43 (65%)
Query: 99 LLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
+L + F+ L+ +Q +EL+ L L +QV+ WFQN+R +SK
Sbjct: 36 VLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 37.0 bits (84), Expect = 0.010, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNP----KQKEELATQLKLKPRQVEVWFQNRRARSK 141
RK+ +K+ + +L E F ++H NP + KEELA + + QV WF N+R R K
Sbjct: 3 RKRRNFNKQATEILNEYF-YSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNP----KQKEELATQLKLKPRQVEVWFQNRRARSK 141
RK+ +K+ + +L E F ++H NP + KEELA + + QV WF N+R R K
Sbjct: 4 RKRRNFNKQATEILNEYF-YSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 30/53 (56%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139
R + ++EQ LE+ F H + +E LA ++ L +++VWF NRRA+
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 61
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRAR 139
R + + EQ LE F+ + +E+LA ++ L+ +VEVWF+NRRA+
Sbjct: 9 RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%)
Query: 77 SCINVDGGPPRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNR 136
S ++ G R + + Q LE+ F+ H + +E+LA + L +V+VWFQNR
Sbjct: 1 SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 137 RAR 139
RA+
Sbjct: 61 RAK 63
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
L+ F+ L ++ ELA L L QV++WFQN+R++ K
Sbjct: 22 LQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 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 = 36.2 bits (82), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
S EQ L+ F N L +++++L+++L L QV+ WF+N RA+ K
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>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 = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 98 RLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
RL +E ++ N+ P+ + ELA QL L ++VWFQNRR + K
Sbjct: 15 RLEKEFYKENYVSRPR-RCELAAQLNLPESTIKVWFQNRRMKDK 57
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 35.8 bits (81), Expect = 0.023, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 28/41 (68%)
Query: 101 EESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
+ F N L +++++L+++L L Q+++WFQN+RA+ K
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 32/55 (58%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
R++ ++ Q +LE F + +EE+A ++ L +V+VWF+NRRA+ +
Sbjct: 9 RERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 34.7 bits (78), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 88 KKLR--LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
K+LR ++ EQ +L + + + K + +A ++ LK R V+VWFQN RAR +
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARER 73
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 34.7 bits (78), Expect = 0.053, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 91 RLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
R + Q R+L++ F N + E+L+ L L R + VWFQN R +++
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 34.3 bits (77), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
+K++ +K Q + LE + N + ++ ++ L RQV +WFQNRR + K
Sbjct: 3 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 34.3 bits (77), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
+K++ +K Q + LE + N + ++ ++ L RQV +WFQNRR + K
Sbjct: 9 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>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 = 34.3 bits (77), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 85 PPRKKLR--LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSKL 142
P RKK R ++ Q LE+ F L ++ LA LK+ QV+ WFQNRR + +
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWR- 73
Query: 143 KQTEMECE 150
+QT E E
Sbjct: 74 RQTAEERE 81
>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 = 33.9 bits (76), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 102 ESFRHNHTLNPK----QKEELATQLKLKPRQVEVWFQNRRARSKLKQTEME 148
+ R + NP+ KE+L L PR + VWFQN+R + K + M+
Sbjct: 16 HTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIMMK 66
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 33.9 bits (76), Expect = 0.073, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 92 LSKEQSRLLEESFRHNHTLNP----KQKEELATQLKLKPRQVEVWFQNRRARSK 141
++K+ + +L E F ++H NP + KEELA + + QV WF N+R R K
Sbjct: 10 MNKQATEILNEYF-YSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 23/46 (50%)
Query: 92 LSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRR 137
S+ Q LE F L ++ LA L++ QV+ WFQNRR
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>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 = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 81 VDGGPPRKKLRLSKEQS-RL-LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138
++G R+K R S E + R+ LE+SF N ++ +A QL ++ + VWF NRR
Sbjct: 94 IEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQ 153
Query: 139 RSK 141
+ K
Sbjct: 154 KEK 156
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 23/42 (54%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
LE+ F L+ + +LA L L QV+ W+QNRR + K
Sbjct: 32 LEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>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 = 31.6 bits (70), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 81 VDGGPPRKKLRLSKEQS--RLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138
++G R+K R S E + LE+SF N ++ +A QL ++ + VWF NRR
Sbjct: 98 IEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 157
Query: 139 RSK 141
+ K
Sbjct: 158 KEK 160
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 81 VDGGPPRKKLRLSKEQS-RL-LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138
++G R+K R S E + R+ LE+SF N + +A QL ++ + VWF NRR
Sbjct: 95 IEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQ 154
Query: 139 RSK 141
+ K
Sbjct: 155 KEK 157
>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 = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 81 VDGGPPRKKLRLSKEQS-RL-LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138
++G R+K R S E + R+ LE+SF N ++ +A QL ++ + VWF NRR
Sbjct: 97 IEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 156
Query: 139 RSK 141
+ K
Sbjct: 157 KEK 159
>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 = 31.2 bits (69), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 81 VDGGPPRKKLRLSKEQS-RL-LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRA 138
++G R+K R S E + R+ LE+SF N ++ +A QL ++ + VWF NRR
Sbjct: 90 IEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 149
Query: 139 RSK 141
+ K
Sbjct: 150 KEK 152
>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 = 1.2, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 31/49 (63%)
Query: 87 RKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQN 135
R + R++ +Q R+L + F N++ + +Q +E+A + L + ++ WF+N
Sbjct: 9 RPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 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 = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
LE+SF N ++ +A QL ++ + VWF NRR + K
Sbjct: 22 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%)
Query: 86 PRKKLRLSKEQSRLLEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRR 137
P+K ++ Q ++LE+SF + + + L + KL R+++ WF RR
Sbjct: 14 PQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65
>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 = 28.1 bits (61), Expect = 4.3, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 127 RQVEVWFQNRRARSK 141
RQ+++WFQNRR + K
Sbjct: 1 RQIKIWFQNRRMKWK 15
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 28.1 bits (61), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 113 KQKEELATQLKLKPRQVEVWFQNRRARSK 141
+Q +A QL L+ V VWF NRR + K
Sbjct: 124 QQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|2J5U|A Chain A, Mrec Lysteria Monocytogenes
pdb|2J5U|B Chain B, Mrec Lysteria Monocytogenes
Length = 255
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 32/105 (30%), Positives = 46/105 (43%), Gaps = 12/105 (11%)
Query: 142 LKQTEMECEYLKRWFGSLTEQNRRLQREVEELRA----MKVGPPTVISPHSCEPLPASTL 197
LK T E ++LK E+ +L+ EV +L+ +K S +PL AS +
Sbjct: 21 LKNTYTENQHLKERL----EELAQLESEVADLKKENKDLKESLDITDSIRDYDPLNASVI 76
Query: 198 SMCPRCERVTTTAIDKGPT---KVTTASSTPAALSPKVGTPALQS 239
S P IDKG + K A +TP+ L KV T +S
Sbjct: 77 SRNPTNWN-DQVEIDKGSSDGVKPDMAVTTPSGLIGKVTTTGAKS 120
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 27.3 bits (59), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 100 LEESFRHNHTLNPKQKEELATQLKLKPRQVEVWFQNRRARSK 141
LE+SF N ++ +A QL ++ + VWF NRR + K
Sbjct: 16 LEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEK 57
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 26.9 bits (58), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 118 LATQLKLKPRQVEVWFQNRRARSK 141
+A +L L+ V VWF NRR R K
Sbjct: 120 MAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 26.9 bits (58), Expect = 9.3, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 127 RQVEVWFQNRRARSK 141
RQ+++WFQNRR + K
Sbjct: 1 RQIKIWFQNRRMKWK 15
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.312 0.127 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,940,286
Number of Sequences: 62578
Number of extensions: 204805
Number of successful extensions: 490
Number of sequences better than 100.0: 95
Number of HSP's better than 100.0 without gapping: 84
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 402
Number of HSP's gapped (non-prelim): 105
length of query: 240
length of database: 14,973,337
effective HSP length: 96
effective length of query: 144
effective length of database: 8,965,849
effective search space: 1291082256
effective search space used: 1291082256
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)