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= 042627
(237 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 43/66 (65%), Gaps = 4/66 (6%)
Query: 92 RKKLRLTIEQSRLLEDSFKL--HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNE 149
R + T Q +LE+ F++ + ++ + LA++LNLE ++++WFQNRRA KLK++
Sbjct: 3 RPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRA--KLKRSH 60
Query: 150 VDCEFL 155
+ +FL
Sbjct: 61 RESQFL 66
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 43/89 (48%), Gaps = 14/89 (15%)
Query: 67 GSKMSQDDGKAGVGNSNSKRINISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQ 124
GS MS G+ N KR ++ T Q+ LE F+ L++ ++ L
Sbjct: 1 GSHMSD-----GLPNKKRKR-------RVLFTKAQTYELERRFRQQRYLSAPEREHLTSL 48
Query: 125 LNLEPRQVEVWFQNRRARTKLKQNEVDCE 153
+ L P QV++WFQN R +TK QNE E
Sbjct: 49 IRLTPTQVKIWFQNHRYKTKRAQNEKGYE 77
>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 = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 77 AGVGNSNSKRINISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEV 134
A G N KR ++++ T Q+ LE F+ L++ ++ LA + L P QV++
Sbjct: 1 ASDGLPNKKR-----KRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKI 55
Query: 135 WFQNRRARTKLKQNE 149
WFQN R +TK QNE
Sbjct: 56 WFQNHRYKTKRAQNE 70
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 90 SGRKKLRLTIEQSRLLEDSF--KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
S R++ T EQ LE F K + +L + +A L L QV++WFQNRRA+ K
Sbjct: 7 SRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%)
Query: 106 EDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
E F ++ T + + +A LNL RQV++WFQNRR + K
Sbjct: 31 EFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 28/43 (65%), Gaps = 2/43 (4%)
Query: 104 LLEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
LE+ F+ +LNSK+ +A++ + P QV VWF N+R R+K
Sbjct: 19 FLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 5/71 (7%)
Query: 79 VGNSNSKRINISGRKKLR---LTIEQSRLLEDSFKLHTTLNSKQAL--AEQLNLEPRQVE 133
VG ++++ + RK+ R ++I LE F H+ +S++ + AE+LNLE V
Sbjct: 73 VGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVR 132
Query: 134 VWFQNRRARTK 144
VWF NRR R K
Sbjct: 133 VWFCNRRQREK 143
>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 = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 104 LLEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
LE F+ +LNSK+ +A++ + P QV VWF N+R R+K
Sbjct: 19 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 36.6 bits (83), Expect = 0.012, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 91 GRKKLRLTIEQSRL--LEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTK 144
GR+K R+ Q+++ LE FK L++ + LA L L QV++WFQNRR ++K
Sbjct: 1 GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 36.6 bits (83), Expect = 0.012, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 92 RKKLRLTIEQSRLLEDSF--KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+K+ T Q+ LE F ++ T + + +A LNL RQV++WFQNRR + K
Sbjct: 3 KKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>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 = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 3/47 (6%)
Query: 101 QSR-LLEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
Q+R LE F+ +LNSK+ +A++ + P QV VWF N+R R+K
Sbjct: 375 QARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 92 RKKLRLTIEQSRL--LEDSFKL--HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
++K+R Q++L L+D F+ + +L Q L+ LNL +QV+ WFQN+R + K
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 36.6 bits (83), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 94 KLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTK 144
++R + +Q+ LE F+ L+ ++ LA+ L L RQV+ WFQNRRA+ +
Sbjct: 11 QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 104 LLEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
LE F+ +LNSK+ +A++ + P QV VWF N+R R+K
Sbjct: 11 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 38/62 (61%), Gaps = 4/62 (6%)
Query: 93 KKLRLTIEQSRL--LEDSFKL--HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQN 148
++ R T S+L LE +F+ + + +++ LA++ NL +++VWFQNRRAR + +
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78
Query: 149 EV 150
V
Sbjct: 79 SV 80
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 37/58 (63%), Gaps = 3/58 (5%)
Query: 90 SGRK-KLRLTIEQSRLLEDSFK--LHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
SGR+ + T EQ LE+ F+ + + +++ LA +++L +VEVWF+NRRA+ +
Sbjct: 6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 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 = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 16/27 (59%), Positives = 20/27 (74%)
Query: 121 LAEQLNLEPRQVEVWFQNRRARTKLKQ 147
LA+ L L QV++WFQNRR +TK KQ
Sbjct: 37 LAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 35.4 bits (80), Expect = 0.027, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 92 RKKLRLTIEQSRL--LEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTK 144
R+K R+ Q+++ LE FK L++ ++ LA ++L P QV++WFQN R + K
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>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 = 0.044, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 93 KKLRLTI--EQSRLLEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
K+LR TI EQ +L + L + K +A ++ L+ R V+VWFQN RAR +
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARER 73
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 34.7 bits (78), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 89 ISGRKKLRLTIEQS-RL-LEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
+S R+K R +IE + R+ LE SF + S+ +AEQLN+E + VWF NRR + K
Sbjct: 98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>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 = 34.7 bits (78), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 90 SGRKKLRLTIEQSRLLEDSFKLHTTLNSKQ--ALAEQLNLEPRQVEVWFQNRRARTK 144
+ R++ T Q+ LE F + L ++ +A L+L RQ+++WFQNRR + K
Sbjct: 28 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 33.9 bits (76), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 92 RKKLRLTIEQSRLLEDSFKLHT----TLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
R++ R T + + LE + HT T + +A L+L RQ+++WFQNRR + K
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 33.9 bits (76), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 104 LLEDSFKL--HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+L D F+ + +L Q L+ LNL +QV+ WFQN+R ++K
Sbjct: 36 VLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>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 = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 4/60 (6%)
Query: 89 ISGRKKLRLTIEQS-RL-LEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
+S R+K R +IE + R+ LE SF + S++ +A+QLN+E + VWF NRR + K
Sbjct: 97 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 10/75 (13%)
Query: 77 AGVGNSNSKRINISGRKKLRLTIEQSRLLEDSFKLHTTLNS--KQALAEQLNLEPRQVEV 134
G+G+ + R N + R Q LE F + L+ + +A L L QV++
Sbjct: 29 PGLGSPSGLRTNFTTR--------QLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 80
Query: 135 WFQNRRARTKLKQNE 149
WFQNRR + K ++ E
Sbjct: 81 WFQNRRMKQKKRERE 95
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 90 SGRKK-LRLTIEQSRLLEDSFKLH--TTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
SGRKK + + Q R LE + + T + ++ ++ +L RQ+ +WFQNRR + K
Sbjct: 6 SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 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 = 32.7 bits (73), Expect = 0.16, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 3/55 (5%)
Query: 101 QSRLLEDSFKLHTTLNSKQ--ALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCE 153
Q+ LE F + L ++ +A L+L RQ+++WFQNRR + K K+N+ E
Sbjct: 7 QTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK-KENKTKGE 60
>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 = 0.17, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 90 SGRKKLRLTIEQSRLLEDSFKLHTTLNSKQAL--AEQLNLEPRQVEVWFQNRRARTK 144
S R + T Q+ LE F + + ++ + A L+L RQ+++WFQNRR ++K
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L Q+++WFQN+RA+ K
Sbjct: 10 YLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 118 KQALAEQLNLEPRQVEVWFQNRRARTK 144
K+ L E L PR + VWFQN+R + K
Sbjct: 33 KEQLVEMTGLSPRVIRVWFQNKRCKDK 59
>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 = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L Q+++WFQN+RA+ K
Sbjct: 27 YLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 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 = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 121 LAEQLNLEPRQVEVWFQNRRARTK 144
LA LNL R +++WFQNRR + K
Sbjct: 36 LAVMLNLTERHIKIWFQNRRMKWK 59
>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 = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 4/60 (6%)
Query: 89 ISGRKKLRLTIEQS-RL-LEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
+S R+K R +IE + R+ LE SF + S++ +A+QLN+E + VWF NRR + K
Sbjct: 101 LSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 32.3 bits (72), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L Q+++WFQN+RA+ K
Sbjct: 25 YLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>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 = 32.3 bits (72), Expect = 0.24, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 92 RKKLRLTIEQSRLLEDSFKLH----TTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147
RK+ R T + + LE + H T + +A L+L RQ+++WFQNRR + K K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK-KE 60
Query: 148 NEVDCE 153
N+ E
Sbjct: 61 NKTKGE 66
>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 = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 4/60 (6%)
Query: 89 ISGRKKLRLTIEQS-RL-LEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
+S R+K R +IE + R+ LE SF + S++ +A+QLN+E + VWF NRR + K
Sbjct: 100 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 32.3 bits (72), Expect = 0.24, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 92 RKKLRLTIEQSRLLEDSFKL--HTTLNSKQALAEQLNLEPRQVEVWFQNRRAR 142
R + T EQ LE +F+ + + +++ LA++ L +V+VWF NRRAR
Sbjct: 4 RSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 32.0 bits (71), Expect = 0.27, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 36/58 (62%), Gaps = 2/58 (3%)
Query: 92 RKKLRLTIEQSRLLEDSFKL--HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147
R++ T +Q + LE +F+ + +++++ +A NL +V VWF+NRRA+ + ++
Sbjct: 5 RQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 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 = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 4/60 (6%)
Query: 89 ISGRKKLRLTIEQS-RL-LEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
+S R+K R +IE + R+ LE SF + S++ +A+QLN+E + VWF NRR + K
Sbjct: 93 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 152
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 114 TLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
T + ++ ++ NL RQV +WFQNRR + K
Sbjct: 33 TKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 32.0 bits (71), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 92 RKKLRLTIEQSRLLEDSFKL--HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
R + T EQ LE F+ + + +++ LA +++L +++VWF NRRA+ +
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 32.0 bits (71), Expect = 0.33, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 92 RKKLRLTIEQSRLLEDSFKLH----TTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
RK+ R T + + LE + H T + +A L+L RQ+++WFQNRR + K
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 97 LTIEQSRLLEDSF--KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
T Q LE F K + ++ + + L+L QV++WFQNRRA+ K
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|2E4M|A Chain A, Crystal Structure Of Hemagglutinin Subcomponent Complex
(Ha- 33HA-17) From Clostridium Botulinum Serotype D
Strain 4947
pdb|2E4M|B Chain B, Crystal Structure Of Hemagglutinin Subcomponent Complex
(Ha- 33HA-17) From Clostridium Botulinum Serotype D
Strain 4947
Length = 286
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 110 KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCE 160
KL T LNS + L++ LN + + WF + R + ++ NE + KC E
Sbjct: 153 KLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWTIEYNETKSAYTLKCQE 203
>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 = 31.6 bits (70), Expect = 0.36, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 36/58 (62%), Gaps = 2/58 (3%)
Query: 92 RKKLRLTIEQSRLLEDSFKL--HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147
R++ T +Q + LE +F+ + +++++ +A NL +V VWF+NRRA+ + ++
Sbjct: 5 RQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|1QXM|A Chain A, Crystal Structure Of A Hemagglutinin Component (Ha1) From
Type C Clostridium Botulinum
pdb|1QXM|B Chain B, Crystal Structure Of A Hemagglutinin Component (Ha1) From
Type C Clostridium Botulinum
Length = 300
Score = 31.6 bits (70), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 110 KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCE 160
KL T LNS + L++ LN + + WF + R + ++ NE + KC E
Sbjct: 167 KLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQE 217
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 31.6 bits (70), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L Q+++WFQN+RA+ +
Sbjct: 27 YLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>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 = 31.6 bits (70), Expect = 0.41, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 5/66 (7%)
Query: 92 RKKLRLTIEQSRLLEDSFKLH----TTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147
RK+ R T + + LE + H T + +A L L RQ+++WFQNRR + K K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK-KE 60
Query: 148 NEVDCE 153
N+ E
Sbjct: 61 NKTKGE 66
>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 = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L Q+++WFQN RA+ K
Sbjct: 25 YLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|3AH1|A Chain A, Ha1 Subcomponent Of Botulinum Type C Progenitor Toxin
Comple N-Acetylneuramic Acid
pdb|3AH1|B Chain B, Ha1 Subcomponent Of Botulinum Type C Progenitor Toxin
Comple N-Acetylneuramic Acid
pdb|3AH2|A Chain A, Ha1 Subcomponent Of Botulinum Type C Progenitor Toxin
Comple N-Acetylgalactosamine
pdb|3AH2|B Chain B, Ha1 Subcomponent Of Botulinum Type C Progenitor Toxin
Comple N-Acetylgalactosamine
pdb|3AH4|A Chain A, Ha1 Subcomponent Of Botulinum Type C Progenitor Toxin
Comple Galactose
pdb|3AH4|B Chain B, Ha1 Subcomponent Of Botulinum Type C Progenitor Toxin
Comple Galactose
Length = 288
Score = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 110 KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCE 160
KL T LNS + L++ LN + + WF + R + ++ NE + KC E
Sbjct: 155 KLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQE 205
>pdb|3AJ5|A Chain A, Ha1 (Ha33) Subcomponent Of Botulinum Type C Progenitor
Toxin Complexed With N-Acetylgalactosamine, Bound At
Site Ii
pdb|3AJ5|B Chain B, Ha1 (Ha33) Subcomponent Of Botulinum Type C Progenitor
Toxin Complexed With N-Acetylgalactosamine, Bound At
Site Ii
Length = 286
Score = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 27/51 (52%)
Query: 110 KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCE 160
KL T LNS + L++ LN + + WF + R + ++ NE + KC E
Sbjct: 153 KLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQE 203
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 31.2 bits (69), Expect = 0.52, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 25/34 (73%), Gaps = 1/34 (2%)
Query: 117 SKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEV 150
+++ LA ++ L +++VWFQNRRA+ + KQ +V
Sbjct: 28 TREELAMKIGLTEARIQVWFQNRRAKWR-KQEKV 60
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 6/65 (9%)
Query: 93 KKLRLTIE--QSRLLEDSFKLHTTLNSK--QALAEQLNLEPRQVEVWFQNRRARTKLKQN 148
K++R + + Q R ++ F ++ ++K + LA++ L R ++VWFQN AR K ++N
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQN--ARAKFRRN 65
Query: 149 EVDCE 153
+ E
Sbjct: 66 LLRQE 70
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 31.2 bits (69), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 17/24 (70%)
Query: 121 LAEQLNLEPRQVEVWFQNRRARTK 144
LA QLNL ++VWFQNRR + K
Sbjct: 34 LAAQLNLPESTIKVWFQNRRMKDK 57
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 31.2 bits (69), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 92 RKKLRLTIEQSRLLEDSF--KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRAR 142
R++ T Q +LE F + + ++ +A ++NL +V+VWF+NRRA+
Sbjct: 9 RERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
>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 = 30.8 bits (68), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 92 RKKLRLTIEQS-RL-LEDSFKLHTTLNSKQAL--AEQLNLEPRQVEVWFQNRRARTK 144
R+K R +IE + R LE SF + S++ L AEQL++E + VWF NRR + K
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEK 57
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.8 bits (68), Expect = 0.60, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 96 RLTIEQSRLLEDSF--KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
R T Q R+L+D F + + + L+ LNL R + VWFQN R + +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>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 = 30.8 bits (68), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L Q+++WF+N+RA+ K
Sbjct: 27 YLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>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 = 30.8 bits (68), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L Q+++WFQN RA+ K
Sbjct: 25 YLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 30.4 bits (67), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRART 143
+ T +Q L+ +L L Q+++WFQN+RA+
Sbjct: 23 YLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 30.4 bits (67), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 121 LAEQLNLEPRQVEVWFQNRRARTK 144
LAE L L QV+ W+QNRR + K
Sbjct: 50 LAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 30.4 bits (67), Expect = 0.92, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 23/31 (74%)
Query: 117 SKQALAEQLNLEPRQVEVWFQNRRARTKLKQ 147
+++ LA ++ L +++VWFQNRRA+ + ++
Sbjct: 28 TREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 30.4 bits (67), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 92 RKKLRLTIEQS-RL-LEDSFKLHTTLNSKQA--LAEQLNLEPRQVEVWFQNRRARTK 144
R+K R +IE + R+ LE SF + S++ +A+QLN+E + VWF NRR + K
Sbjct: 7 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 30.0 bits (66), Expect = 1.0, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 92 RKKLRLTIEQSRLLEDSFKLHT--TLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+K++ T Q + LE + + T + ++ ++ NL RQV +WFQNRR + K
Sbjct: 3 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 21/29 (72%)
Query: 121 LAEQLNLEPRQVEVWFQNRRARTKLKQNE 149
L+ +L L QV++WF+NRR R K++ ++
Sbjct: 35 LSAKLALGTAQVKIWFKNRRRRHKIQSDQ 63
>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 = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L Q+++WF N+RA+ K
Sbjct: 23 YLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>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 = 30.0 bits (66), Expect = 1.3, Method: Composition-based stats.
Identities = 14/34 (41%), Positives = 25/34 (73%), Gaps = 1/34 (2%)
Query: 117 SKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEV 150
+++ LA ++ L +++VWFQNRRA+ + KQ +V
Sbjct: 35 TREELAMKIGLTEARIQVWFQNRRAKWR-KQEKV 67
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 29.6 bits (65), Expect = 1.4, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ L + LA L L QV++WFQN+R++ K
Sbjct: 31 YLALPERAELAASLGLTQTQVKIWFQNKRSKIK 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 = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 22/30 (73%)
Query: 115 LNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ +++ LA + +L +V+VWFQNRRA+ +
Sbjct: 36 VYAREQLAMRTDLTEARVQVWFQNRRAKWR 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 = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 92 RKKLRLTIEQSRL--LEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRR 140
RKK R + + ++ LE F L S + ALA L + QV+ WFQNRR
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRR 69
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 120 ALAEQLNLEPRQVEVWFQNRRARTK 144
LA+ L LE V VWF NRR + K
Sbjct: 131 GLADSLQLEKEVVRVWFCNRRQKEK 155
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 105 LEDSFKLHTTLNS--KQALAEQLNLEPRQVEVWFQNRRARTK 144
LE F L S + ALA+ L + QV+ WFQNRR + +
Sbjct: 12 LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>pdb|3AJ6|A Chain A, Ha1 (Ha33) Mutant F179i Of Botulinum Type C Progenitor
Toxin Complexed With N-Acetylgalactosamine, Bound At
Site Ii
pdb|3AJ6|B Chain B, Ha1 (Ha33) Mutant F179i Of Botulinum Type C Progenitor
Toxin Complexed With N-Acetylgalactosamine, Bound At
Site Ii
Length = 286
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%)
Query: 110 KLHTTLNSKQALAEQLNLEPRQVEVWFQNRRARTKLKQNEVDCEFLKKCCE 160
KL T LNS + L++ LN + + W + R + ++ NE + KC E
Sbjct: 153 KLQTQLNSDRFLSKNLNSQIIVLWQWIDSSRQKWIIEYNETKSAYTLKCQE 203
>pdb|2ECB|A Chain A, The Solution Structure Of The Third Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein
Length = 89
Score = 28.5 bits (62), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 32/102 (31%), Positives = 48/102 (47%), Gaps = 22/102 (21%)
Query: 80 GNSNSKRINISGRKKLRLTIEQSRLLEDSFKLHTTLNSKQALAEQLNLEPRQVEVWFQNR 139
G+S S + + +K T EQ R+L+ SF LNS E+LN
Sbjct: 1 GSSGSSGPDFTPQKFKEKTAEQLRVLQASF-----LNSSVLTDEELN-----------RL 44
Query: 140 RARTKLKQNEVDCEFLKKCCESLTDENKRLKKELQELQSAKA 181
RA+TKL + E+D F +K ++K LK+E E+ + A
Sbjct: 45 RAQTKLTRREIDAWFTEK------KKSKALKEEKMEIDESNA 80
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 28.5 bits (62), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 121 LAEQLNLEPRQVEVWFQNRRARTK 144
+A QL LE V VWF NRR + K
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 28.1 bits (61), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 100 EQSRLLEDSFKLHTTLNS---KQALAEQLNLEPRQVEVWFQNRRAR 142
E+SR + + H S K+ LAE L QV WF+NRR R
Sbjct: 503 EKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 27.7 bits (60), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 112 HTTLNSKQALAEQLNLEPRQVEVWFQNRRARTK 144
+ T +Q L+ +L L QV+ WF+N RA+ K
Sbjct: 28 YLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>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 = 26.9 bits (58), Expect = 8.9, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 130 RQVEVWFQNRRARTK 144
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
0.313 0.127 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,512,170
Number of Sequences: 62578
Number of extensions: 246610
Number of successful extensions: 517
Number of sequences better than 100.0: 87
Number of HSP's better than 100.0 without gapping: 80
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 433
Number of HSP's gapped (non-prelim): 89
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
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)