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= 024915
(260 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 = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 36/57 (63%)
Query: 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
SP+ K ++ A LE+ F+ +L+ K+K+ +A+K + P QV VWF N+R RSK
Sbjct: 5 SPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 92 HHEDEGGSPRKKLRLTKPQFAT---LEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQ 148
++E G + RK+ R T A LE F EHS S ++ +AE+LNL V VWF
Sbjct: 77 YNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFC 136
Query: 149 NRRARSK 155
NRR R K
Sbjct: 137 NRRQREK 143
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 37/64 (57%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTE 160
++++ TK Q LE F++ LS +++ LA + L P QV++WFQN R ++K Q E
Sbjct: 11 KRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE 70
Query: 161 VECE 164
E
Sbjct: 71 KGYE 74
>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 = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
SP+ K ++ A LE F+ +L+ K+K+ +A+K + P QV VWF N+R RSK
Sbjct: 5 SPKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 33/53 (62%)
Query: 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
++R + Q LE F+ LSP +++ LA+ L L RQV+ WFQNRRA+ +
Sbjct: 11 QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 36/64 (56%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTE 160
++++ TK Q LE F++ LS +++ L + L P QV++WFQN R ++K Q E
Sbjct: 14 KRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQNE 73
Query: 161 VECE 164
E
Sbjct: 74 KGYE 77
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 29/44 (65%)
Query: 112 ATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
A LE F+ +L+ K+K+ +A+K + P QV VWF N+R RSK
Sbjct: 378 AFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 36/64 (56%), Gaps = 2/64 (3%)
Query: 94 EDEGGSPRKKLR--LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRR 151
ED+ ++K R + Q L D F+ LS +Q Q L+ LNL +QV+ WFQN+R
Sbjct: 15 EDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQR 74
Query: 152 ARSK 155
+SK
Sbjct: 75 MKSK 78
>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 = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%)
Query: 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
G + + ++ Q L+D F++ LS +Q Q L+ LNL +QV+ WFQN+R + K
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/44 (45%), Positives = 29/44 (65%)
Query: 112 ATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
A LE F+ +L+ K+K+ +A+K + P QV VWF N+R RSK
Sbjct: 10 AFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTE 160
R + T+ Q LE+ F+ + + LA+KLNL ++++WFQNRRA KLK++
Sbjct: 3 RPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRA--KLKRSH 60
Query: 161 VECELL 166
E + L
Sbjct: 61 RESQFL 66
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 34/55 (61%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
++++ ++ Q LE FK+ LS +++ LA ++L P QV++WFQN R + K
Sbjct: 4 KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
G + ++ ++ Q LE FK+ LS ++ LA L L QV++WFQNRR +SK
Sbjct: 1 GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+ Q A L+ F E+ L+ +++Q L+ +L L Q+++WFQN+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 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 = 7e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 31/59 (52%)
Query: 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
G S R++ T Q LE F LS ++ +A L L QV++WFQNRRA+ K
Sbjct: 5 GKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 29/54 (53%)
Query: 110 QFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVEC 163
Q LE F LS ++ LA+ L L QV++WFQNRR ++K KQ E
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSEL 68
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 36/61 (59%)
Query: 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158
S R + T+ Q LE F + ++ +++ +A L+L RQ+++WFQNRR +SK +
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDR 62
Query: 159 T 159
T
Sbjct: 63 T 63
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+ Q A L+ F E+ L+ +++Q L+ +L L Q+++WFQN+RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
T Q LE F++ LS ++ + L+L QV++WFQNRRA++K
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
R + T Q LE+ F+E ++ LA K++LR +VEVWF+NRRA+ +
Sbjct: 9 RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 90 RDHHEDEGGSP--RKKLR--LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEV 145
R H + +P RKK R T+ Q A LE F + L+ ++ LA L + QV+
Sbjct: 4 RIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKT 63
Query: 146 WFQNRRARSKLKQTEVECELLKRCCEKL 173
WFQNRR + + +QT E E ++ +L
Sbjct: 64 WFQNRRTKWR-RQTAEEREAERQAANRL 90
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 35/54 (64%), Gaps = 2/54 (3%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159
+ Q A L+ F E+ L+ +++Q L+ +L L Q+++WFQN AR+K+K++
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQN--ARAKIKKS 59
>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 = 17/48 (35%), Positives = 31/48 (64%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153
+ Q A L+ F E+ L+ +++Q L+ +L L Q+++WFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+ Q A L+ F E+ L+ +++Q L+ +L L Q+++WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
G + R++ T+ Q LE F + L+ +++ +A L+L RQ+++WFQNRR + K
Sbjct: 26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 32/60 (53%)
Query: 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLK 157
G R + T Q A LE F + L+ + L+ KL 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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 32/50 (64%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+ Q A L+ F E+ L+ +++Q L+ +L L Q+++WF+N+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153
G R + + Q A + F E+ L+ +++Q L+ +L L Q+++WFQN+RA+
Sbjct: 1 GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 93 HEDEGGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152
H EG +K++ TK Q LE + + ++ +++ ++ NL RQV +WFQNRR
Sbjct: 3 HMLEG--RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60
Query: 153 RSK 155
+ K
Sbjct: 61 KEK 63
>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 = 0.004, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156
G + R + T+ Q LE F + +S ++ LA LNL R +++WFQNRR + K
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 157 KQ 158
++
Sbjct: 61 EE 62
>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 = 0.004, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+ Q A L+ F E+ L+ +++Q L+ +L L Q+++WF N+RA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 29/49 (59%)
Query: 107 TKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
TK Q LE F + L+ ++ +A LNL RQV++WFQNRR + K
Sbjct: 21 TKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>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 = 24/78 (30%), Positives = 41/78 (52%), Gaps = 5/78 (6%)
Query: 89 IRDHHEDEGGSPRKKLRLTKPQFAT-----LEDTFKEHSTLSPKQKQGLAEKLNLRPRQV 143
I D + G + ++K R ++ F+ LE F+ ++ LA++ NL ++
Sbjct: 3 ISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARI 62
Query: 144 EVWFQNRRARSKLKQTEV 161
+VWFQNRRAR + + T V
Sbjct: 63 QVWFQNRRARLRKQHTSV 80
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 32/55 (58%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
R + T+ Q LE F + L+ +++ +A L+L RQ+++WFQNRR + K
Sbjct: 22 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 37.4 bits (85), Expect = 0.008, Method: Composition-based stats.
Identities = 22/55 (40%), Positives = 32/55 (58%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+K+ TK Q LE F + L+ ++ +A LNL RQV++WFQNRR + K
Sbjct: 3 KKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 29/55 (52%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
R + T+ Q LE F++ LS + LAE L L QV+ W+QNRR + K
Sbjct: 19 RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 36.6 bits (83), Expect = 0.013, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+K++ TK Q LE + + ++ +++ ++ NL RQV +WFQNRR + K
Sbjct: 3 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>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 = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
T+ Q LE F + + +S ++ LA +LNL ++VWFQNRR + K
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 92 HHEDEGGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRR 151
H ++G R + T Q LE F++ ++ LA + +L +V+VWFQNRR
Sbjct: 2 HMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRR 61
Query: 152 ARSK 155
A+ +
Sbjct: 62 AKWR 65
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 36.2 bits (82), Expect = 0.017, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 31/55 (56%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
R++ T+ Q LE F + ++ +A K+NL +V+VWF+NRRA+ +
Sbjct: 9 RERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 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 = 0.017, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 98 GSPRKKLR--LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
GS K+ R + Q A L+ F E+ L+ +++Q L+ +L L QV+ WF+N RA+ K
Sbjct: 1 GSDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 98 GSPRK-KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156
GSP + T Q LE F + LS ++ +A L L QV++WFQNRR + K
Sbjct: 32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
Query: 157 KQTE 160
++ E
Sbjct: 92 RERE 95
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 35.8 bits (81), Expect = 0.027, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156
G R++ T Q LE TF+ + ++ +A NL +V VWF+NRRA+ +
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 157 KQ 158
++
Sbjct: 61 RE 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 = 35.4 bits (80), Expect = 0.029, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156
G R++ T Q LE TF+ + ++ +A NL +V VWF+NRRA+ +
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 157 KQ 158
++
Sbjct: 61 RE 62
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 35.0 bits (79), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%)
Query: 110 QFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
Q A L+ F++ L+ ++ LA L L QV++WFQN+R++ K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 35.0 bits (79), Expect = 0.040, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 101 RKKLRLTKPQFATLE--DTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
RK+ R T ++ TLE F + L+ +++ +A L+L RQ+++WFQNRR + K
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 34.7 bits (78), Expect = 0.048, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 32/55 (58%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+K++ +K Q LE + + ++ +++ ++ +L RQ+ +WFQNRR + K
Sbjct: 9 KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>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 = 34.7 bits (78), Expect = 0.049, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 107 TKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
T+ Q LE F + L+ +++ +A L+L RQ+++WFQNRR + K
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>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 = 34.7 bits (78), Expect = 0.053, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 101 RKKLRLTKPQFATLE--DTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
RK+ R T ++ TLE F + L+ +++ +A L+L RQ+++WFQNRR + K
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 34.7 bits (78), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 112 ATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159
L + + + SP++K+ LAE L QV WF+NRR R + +
Sbjct: 507 GVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEA 554
>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 = 33.9 bits (76), Expect = 0.085, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 101 RKKLRLTKPQFATLE--DTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
RK+ R T ++ TLE F + L+ +++ +A L L RQ+++WFQNRR + K
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 58
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 33.9 bits (76), Expect = 0.092, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
R T Q L+D F ++ + + L+ LNL R + VWFQN R +++
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 33.9 bits (76), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%)
Query: 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRR 151
++ Q LE F L+ ++ LA+ L + QV+ WFQNRR
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>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 = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%)
Query: 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+ R + L + Q TL + + K+ L E L PR + VWFQN+R + K
Sbjct: 3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDK 59
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 27/56 (48%)
Query: 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153
G R + T Q LE F+ ++ LA++ L +V+VWF NRRAR
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 33.1 bits (74), Expect = 0.15, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 27/38 (71%)
Query: 118 FKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
F E+ L+ +++Q L+ +L L Q+++WFQN+RA+ K
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 32.7 bits (73), Expect = 0.19, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 26/53 (49%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153
R + T Q LE F ++ LA K+ L +++VWFQNRRA+
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 53
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 96 EGGSPRKKLRL---TKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152
EG S R+K R T + A LE +F E+ + + +AE+LN+ + VWF NRR
Sbjct: 96 EGLSRRRKKRTSIETNIRVA-LEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQ 154
Query: 153 RSK 155
+ K
Sbjct: 155 KEK 157
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 98 GSPRKKLRLT--KPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153
GS K++R + Q T++ F + K + LA+K L R ++VWFQN RA+
Sbjct: 4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 102 KKLR--LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
K+LR +T Q L + S + K +A ++ L+ R V+VWFQN RAR +
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARER 73
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+ T Q LE F ++ LA K+ L +++VWFQNRRA+ +
Sbjct: 4 MTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 32.0 bits (71), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 96 EGGSPRKKLRL---TKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152
EG S R+K R T + A LE +F E+ + ++ +A++LN+ + VWF NRR
Sbjct: 95 EGLSRRRKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQ 153
Query: 153 RSK 155
+ K
Sbjct: 154 KEK 156
>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 = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 91 DHHEDEGGSPRK-KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQN 149
+H +D G +P+K +L T Q TL FKE+ S + + ++++L L V +F N
Sbjct: 88 EHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN 147
Query: 150 RRARS 154
R RS
Sbjct: 148 ARRRS 152
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 29/55 (52%)
Query: 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
R + T+ Q LE F+ ++ LA K++L +++VWF NRRA+ +
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
>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 = 31.2 bits (69), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 99 SPRKKLRLTKPQFAT-----LEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153
+P++K R + F + LE F ++ LA K+ L +++VWFQNRRA+
Sbjct: 1 APKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 60
Query: 154 SK 155
+
Sbjct: 61 WR 62
>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 = 30.8 bits (68), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 96 EGGSPRKKLRL---TKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152
EG S R+K R T + A LE +F E+ + ++ +A++LN+ + VWF NRR
Sbjct: 91 EGLSRRRKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 149
Query: 153 RSK 155
+ K
Sbjct: 150 KEK 152
>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 = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 96 EGGSPRKKLRL---TKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152
EG S R+K R T + A LE +F E+ + ++ +A++LN+ + VWF NRR
Sbjct: 99 EGLSERRKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 157
Query: 153 RSK 155
+ K
Sbjct: 158 KEK 160
>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 = 30.8 bits (68), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 96 EGGSPRKKLRL---TKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152
EG S R+K R T + A LE +F E+ + ++ +A++LN+ + VWF NRR
Sbjct: 98 EGLSRRRKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 156
Query: 153 RSK 155
+ K
Sbjct: 157 KEK 159
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 21/44 (47%)
Query: 112 ATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
LE F + S + GLA+ L L V VWF NRR + K
Sbjct: 112 GALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 91 DHHEDEGGSPRK-KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQN 149
+H +D G +P+K +L T Q TL FKE+ S + + ++++L L V +F N
Sbjct: 86 EHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMN 145
Query: 150 RR 151
R
Sbjct: 146 AR 147
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 29.3 bits (64), Expect = 2.1, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 114 LEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
LE +F E+ + ++ +A++LN+ + VWF NRR + K
Sbjct: 22 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 28.5 bits (62), Expect = 4.4, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 101 RKKLRLTKPQFATLEDTFKEHST---LSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
RK+ K L + F H + S + K+ LA+K + QV WF N+R R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 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 = 4.9, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 101 RKKLRLTKPQFATLEDTFKEHST---LSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
RK+ K L + F H + S + K+ LA+K + QV WF N+R R K
Sbjct: 4 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 101 RKKLRLTKPQFATLEDTFKEH-STLSPKQ--KQGLAEKLNLRPRQVEVWFQNRRARSK 155
RK+ K L + F H S P + K+ LA+K + QV WF N+R R K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 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 = 28.1 bits (61), Expect = 5.1, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 101 RKKLRLTKPQFATLEDTFKEHST---LSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
RK+ +K L + F H + S + K+ LA K + QV WF N+R R K
Sbjct: 3 RKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1HJB|A Chain A, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|B Chain B, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|D Chain D, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|E Chain E, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
Length = 87
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 138 LRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQREVQELKSMKLSGAPL 197
+R + + + R ++K++ E + ++L+ L EN+RLQ++V++L + L
Sbjct: 18 IRRERNNIAVRKSRDKAKMRNLETQHKVLE-----LTAENERLQKKVEQLSRELSTLRNL 72
Query: 198 YMKLPAPTLTVCPSC 212
+ +LP P L C
Sbjct: 73 FKQLPEPLLASSGHC 87
>pdb|2ECB|A Chain A, The Solution Structure Of The Third Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein
Length = 89
Score = 27.7 bits (60), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 33/66 (50%)
Query: 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158
+P+K T Q L+ +F S L+ ++ L + L R+++ WF ++ LK+
Sbjct: 11 TPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKE 70
Query: 159 TEVECE 164
++E +
Sbjct: 71 EKMEID 76
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 113 TLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155
+LE F + S +Q +A +L L V VWF NRR + K
Sbjct: 110 SLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
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
0.314 0.131 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,262,475
Number of Sequences: 62578
Number of extensions: 207814
Number of successful extensions: 498
Number of sequences better than 100.0: 94
Number of HSP's better than 100.0 without gapping: 88
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 409
Number of HSP's gapped (non-prelim): 95
length of query: 260
length of database: 14,973,337
effective HSP length: 97
effective length of query: 163
effective length of database: 8,903,271
effective search space: 1451233173
effective search space used: 1451233173
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)