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= 028655
(206 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 7/66 (10%)
Query: 83 FDGWL---GQSGKKRRLTATQVQF----LERNFEVENKLEPERKVQLAKELGLQPRQVAI 135
F W+ G +G +RR T ++ LE+ F + L R++++A L L RQ+ I
Sbjct: 7 FYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKI 66
Query: 136 WFQNRR 141
WFQNRR
Sbjct: 67 WFQNRR 72
>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 = 24/51 (47%), Positives = 30/51 (58%)
Query: 95 RLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
R + Q LE+ FE + L P + +LAK L L RQV WFQNRRA+ R
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 31/54 (57%)
Query: 99 TQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKD 152
TQV LER F + L + LAK L L QV IWFQNRR +++ ++L +
Sbjct: 14 TQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67
>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 = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 91 GKKRRLTATQVQFLE--RNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQR 148
K+ R T T+ Q LE + F + R++ +A L L RQ+ IWFQNRR +S+ R
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDR 62
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 85 GWL-GQSGKKRRLTATQVQFLE--RNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRR 141
WL +S +K+R T+ Q LE + F L +R+ ++A+ L L RQV IWFQNRR
Sbjct: 6 NWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRR 65
Query: 142 ARSRNQRLGKD 152
+ +++ KD
Sbjct: 66 MKM--KKINKD 74
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 85 GWLGQSGKKRRLTATQVQF--LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRA 142
G G SG+K R + Q L+R F+ L + +LA LGL QV IWFQN+R+
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 143 R 143
+
Sbjct: 61 K 61
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 85 GWLGQSGKKRRL--TATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRA 142
G G SG+K+R+ + Q++ LER + + +++ +++ L RQ+ IWFQNRR
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV 60
Query: 143 RSR 145
+ +
Sbjct: 61 KEK 63
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 34/69 (49%)
Query: 79 AYVDFDGWLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQ 138
A V G SG + T Q+ LE+ F L R+V++A L L QV IWFQ
Sbjct: 24 AKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQ 83
Query: 139 NRRARSRNQ 147
NRR + + +
Sbjct: 84 NRRMKQKKR 92
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 91 GKKRRLTATQVQF--LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
G+K+R+ T+VQ LER + + +++ +++ L RQV IWFQNRR + +
Sbjct: 7 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 92 KKRRLTATQVQFLE--RNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
K++R + T+ Q LE + F L R++++A L L RQ+ IWFQNRR +
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82
>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 = 40.8 bits (94), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 92 KKRRLTATQVQFLE--RNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149
K+ R T T+ Q LE + F L R++++A L L RQ+ IWFQNRR + + +
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
Query: 150 GK 151
K
Sbjct: 63 TK 64
>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 = 40.8 bits (94), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 92 KKRRLTATQVQFLE--RNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149
K+ R T T+ Q LE + F L R++++A L L RQ+ IWFQNRR + + +
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
Query: 150 GK 151
K
Sbjct: 63 TK 64
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 91 GKKRR----LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146
GK RR T+ Q+ LE+ F + L + Q+A L L QV IWFQNRRA+ +
Sbjct: 5 GKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
Query: 147 QRLG 150
+ G
Sbjct: 65 IKAG 68
>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 = 6e-04, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 92 KKRRLTATQVQFLE--RNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
K+ R T T+ Q LE + F L R++++A L L RQ+ IWFQNRR + + +
Sbjct: 4 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>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 = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 103 FLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
FLE+ F + L + K ++AK+ G+ P QV +WF N+R RS+
Sbjct: 379 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 6e-04, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 29/55 (52%)
Query: 97 TATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGK 151
T Q LE+ F L R++++A L L RQ+ IWFQNRR + + + K
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 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 = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 29/48 (60%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
++ Q+ L+R F L R+ QL+ ELGL Q+ IWFQN+RA+
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 91 GKKRRLTATQVQF--LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
G+K+R+ T+VQ LER + + +++ +++ L RQV IWFQNRR + +
Sbjct: 1 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 29/48 (60%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
++ Q+ L+R F L R+ QL+ ELGL Q+ IWFQN+RA+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 55
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 89 QSGKKRRLTATQVQF--LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
+ G++ R T++Q LE+ FE + L ++ LA+ LGL QV W+QNRR +
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 29/48 (60%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
++ Q+ L+R F L R+ QL+ ELGL Q+ IWFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 35/59 (59%), Gaps = 4/59 (6%)
Query: 92 KKRRLTATQVQF--LERNFEVENKLE-PERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
+KRR+ +Q Q LER F+ + L PER+ LA + L P QV IWFQN R + + Q
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPERE-HLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 84 DGWLGQSGKKRRLTATQVQF--LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRR 141
DG L +KRR+ T+ Q LER F + L + LA + L P QV IWFQN R
Sbjct: 3 DG-LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHR 61
Query: 142 ARSRNQRLGKDYD 154
+++ + K Y+
Sbjct: 62 YKTKRAQNEKGYE 74
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQR 148
T Q+ LE+ F EN + R+ +LA +L L + +WFQNRR + + QR
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 39.7 bits (91), Expect = 0.001, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 92 KKRRLTATQVQFLE--RNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
+K+R T+ Q LE + F L +R+ ++A+ L L RQV IWFQNRR + +
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
++ Q+ L+R F L R+ QL+ ELGL Q+ IWFQN RA+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAK 55
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
++ Q+ L+R F L R+ QL+ ELGL Q+ IWF+N+RA+
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAK 57
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 29/50 (58%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
++ Q+ +R F L R+ QL+ ELGL Q+ IWFQN+RA+ R
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 103 FLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
FLE+ F + L + K ++AK+ G+ P QV +WF N+R RS+
Sbjct: 11 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
++ Q+ L+R F L R+ QL+ ELGL Q+ IWFQN RA+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 55
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 28/43 (65%)
Query: 103 FLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
FLE+ F + L + K ++AK+ G+ P QV +WF N+R RS+
Sbjct: 19 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 22/56 (39%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 90 SGKKRRLTATQVQFLE--RNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
S K+ R T+ Q LE + F + R+V+LA L L R + IWFQNRR +
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMK 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 38.5 bits (88), Expect = 0.003, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 33/57 (57%)
Query: 91 GKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
G T+ Q++ LE+ F + + + +LA ++GL ++ +WFQNRRA+ R Q
Sbjct: 1 GSHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 28/50 (56%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
+ QV LER F+ + L + QLA L L QV IWFQNRR +S+
Sbjct: 9 FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 84 DGWLGQSGKKRRLTATQVQF--LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRR 141
DG L +KRR+ T+ Q LER F + L + L + L P QV IWFQN R
Sbjct: 6 DG-LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHR 64
Query: 142 ARSRNQRLGKDYD 154
+++ + K Y+
Sbjct: 65 YKTKRAQNEKGYE 77
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 27/43 (62%)
Query: 103 FLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
FLE F + L + K ++AK+ G+ P QV +WF N+R RS+
Sbjct: 19 FLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 0.004, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 28/48 (58%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
++ Q+ L+R F L R+ QL+ ELGL Q+ IWF N+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAK 53
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 6/61 (9%)
Query: 89 QSGKKRRLTAT--QVQFLERNFEVENKLEPERKV--QLAKELGLQPRQVAIWFQNRRARS 144
Q K+ R T T Q++ L + + +++ P RK+ +A E+GL+ R V +WFQN RAR
Sbjct: 15 QRDKRLRTTITPEQLEILYQKYLLDSN--PTRKMLDHIAHEVGLKKRVVQVWFQNTRARE 72
Query: 145 R 145
R
Sbjct: 73 R 73
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 24/39 (61%)
Query: 105 ERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
+R F L R+ QL+ ELGL Q+ IWFQN+RA+
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 40
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 88 GQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
GQ + TA Q++ LER FE + + + +LA+ L +V +WF NRRAR R Q
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146
T Q+ LER F + L + + + L L QV IWFQNRRA+++
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 30/52 (57%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
+A+Q+ LER FE + + +LA+ L ++ +WFQNRRAR R Q
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 37.0 bits (84), Expect = 0.008, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 32/52 (61%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
T+ Q++ LE+ F + + + +LA ++GL ++ +WFQNRRA+ R Q
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 36.6 bits (83), Expect = 0.010, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 88 GQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
G + T++Q+ LE++F L R L+ +L L QV IWF+NRR R + Q
Sbjct: 1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 87 LGQSGKKRR----LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRA 142
+ GKKRR T+ Q++ LE+ F+ + + + QLA L +V +WFQNRRA
Sbjct: 3 MSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRA 62
Query: 143 RSRN-QRLGK 151
+ R +R G+
Sbjct: 63 KWRKRERFGQ 72
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 26/49 (53%)
Query: 99 TQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
+QV LER F + L + LAK L + QV WFQNRR + R Q
Sbjct: 7 SQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 36.2 bits (82), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 88 GQSGKKRR--LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
G SG++ R T Q++ LE F+ + + QLA+++ L+ +V +WF+NRRA+ R
Sbjct: 4 GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 85 GWLGQSGKKRRLT--ATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRA 142
G G SGK+ R + Q++ ++ F + + + + QLA++ GL R + +WFQN RA
Sbjct: 1 GSSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARA 60
Query: 143 RSR 145
+ R
Sbjct: 61 KFR 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 = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 27/48 (56%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
++ Q+ L+R F L R+ QL+ ELGL QV WF+N RA+
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAK 58
>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 = 35.0 bits (79), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 26/52 (50%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
T QV LE+ F + L + LA+ L + QV WFQNRR + R Q
Sbjct: 24 FTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
>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 = 34.3 bits (77), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 32/52 (61%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
T+ Q++ LE+ F + + + +LA ++GL ++ +WFQNRRA+ R Q
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 33.9 bits (76), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 88 GQSGKKRR--LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
G SG++ R T Q++ LE+ FE + + + +LA ++ L ++ +WF NRRA+ R
Sbjct: 4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
Query: 146 NQ 147
+
Sbjct: 64 RE 65
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
Length = 96
Score = 33.9 bits (76), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 28/62 (45%)
Query: 88 GQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
G +GK + T Q+ L+ F PE +LAKE GL + WF + R +N
Sbjct: 24 GSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG 83
Query: 148 RL 149
L
Sbjct: 84 NL 85
>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: Composition-based stats.
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149
L Q+ L + + + K QL + GL PR + +WFQN+R + + + +
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 33.5 bits (75), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 15/30 (50%), Positives = 19/30 (63%)
Query: 116 PERKVQLAKELGLQPRQVAIWFQNRRARSR 145
P K +LA+ GL QV+ WF+NRR R R
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQRDR 550
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 33.5 bits (75), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 92 KKRRLTATQV--QFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
+KRR T + LER+F +K + +++A+EL L+ V +WF NRR R +
Sbjct: 88 RKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>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 = 33.1 bits (74), Expect = 0.10, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 92 KKRRLTATQVQF-LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
KKR T V+F LE++F K E + +A++L ++ + +WF NRR + +
Sbjct: 3 KKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEK 57
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 96 LTATQVQFLERNFEVENKL-EPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
+T QV+ LE NF NK +P +A E GL Q WF+ R A R
Sbjct: 8 MTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 32.7 bits (73), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 85 GWLGQSGKKRRLTATQVQF--LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRA 142
G G SG++ R T T+ Q LE F + + ++A ++ L +V +WF+NRRA
Sbjct: 1 GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRA 60
Query: 143 RSR 145
+ R
Sbjct: 61 KCR 63
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 85 GWLGQSGKK--RRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQN 139
G G SGK+ R+T Q++ L + F++ N E+ ++A + GL + + WF+N
Sbjct: 1 GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 32.3 bits (72), Expect = 0.19, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 32/59 (54%)
Query: 89 QSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147
Q ++ T+ Q+Q LE F+ + + + ++A L +V +WF+NRRA+ R +
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143
T Q++ LE F V + LA++L L+ ++ IWFQNRRA+
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAK 55
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 95 RLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
R T Q++ L+ F+ + + QL+ L L R + +WFQN R ++R
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 30.8 bits (68), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
++TQ+ L F+ + L ++ +L+ L L +QV WFQN+R +S+
Sbjct: 29 FSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 30.8 bits (68), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146
L+A + F F ++++E L K GL R+V WF +RR RN
Sbjct: 20 LSALKGSFCRNQFPGQSEVE-----HLTKVTGLSTREVRKWFSDRRYHCRN 65
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 117 ERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGK 151
E K +LAK+ G+ QV+ WF N+R R + + +GK
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK-KNIGK 65
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 29.6 bits (65), Expect = 1.4, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 92 KKRRLTATQVQF-LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
KKR T ++ LE++F K E +A +L ++ + +WF NRR + +
Sbjct: 9 KKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 117 ERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGK 151
E K +LAK+ G+ QV+ WF N+R R + + +GK
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK-KNIGK 65
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 28.9 bits (63), Expect = 2.0, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 117 ERKVQLAKELGLQPRQVAIWFQNRRARSR 145
E K +LAK+ G+ QV+ WF N+R R +
Sbjct: 34 EAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>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 = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 87 LGQSGKKRRLTATQVQF-LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
L + KKR T ++ LE++F K E +A +L ++ + +WF NRR + +
Sbjct: 101 LSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 28.9 bits (63), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 87 LGQSGKKRRLTATQVQF-LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
L + KKR T ++ LE++F K E +A +L ++ + +WF NRR + +
Sbjct: 97 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 117 ERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGK 151
E K +LAK+ G+ QV+ WF N+R R + + +GK
Sbjct: 33 EAKEELAKKSGITVSQVSNWFGNKRIRYK-KNIGK 66
>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 = 2.5, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 70 FQSLDNEDNAYVDFDGWLGQSGKKRRLTATQVQF---LERNFEVENKLEPERKVQLAKEL 126
+ D+ + + D Q K+++ T+ +V LE +F K LA L
Sbjct: 77 LEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSL 136
Query: 127 GLQPRQVAIWFQNRRARSR 145
L+ V +WF NRR + +
Sbjct: 137 QLEKEVVRVWFCNRRQKEK 155
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 87 LGQSGKKRRLTATQVQF-LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
L + KKR T ++ LE++F K E +A++L ++ + +WF NRR + +
Sbjct: 98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>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 = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 87 LGQSGKKRRLTATQVQF-LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
L + KKR T ++ LE++F K E +A +L ++ + +WF NRR + +
Sbjct: 93 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 152
>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 = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 87 LGQSGKKRRLTATQVQF-LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
L + KKR T ++ LE++F K E +A +L ++ + +WF NRR + +
Sbjct: 100 LSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 90 SGKKRRLTATQVQF--LERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
+ +K R +Q Q L+ F+ + L ++ +L+ L L +QV WFQN+R + +
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|2FOK|A Chain A, Structure Of Restriction Endonuclease Foki
pdb|2FOK|B Chain B, Structure Of Restriction Endonuclease Foki
Length = 579
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 85 GWLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARS 144
GW+ GK L VQ +RN +V N+++ + L KE +Q VAI Q+ +
Sbjct: 9 GWVQNPGKFENLKRV-VQVFDRNSKVHNEVKNIKIPTLVKESKIQKELVAIMNQHDLIYT 67
Query: 145 RNQRLG 150
+ +G
Sbjct: 68 YKELVG 73
>pdb|1FOK|A Chain A, Structure Of Restriction Endonuclease Foki Bound To Dna
Length = 576
Score = 28.1 bits (61), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 85 GWLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARS 144
GW+ GK L VQ +RN +V N+++ + L KE +Q VAI Q+ +
Sbjct: 6 GWVQNPGKFENLKRV-VQVFDRNSKVHNEVKNIKIPTLVKESKIQKELVAIMNQHDLIYT 64
Query: 145 RNQRLG 150
+ +G
Sbjct: 65 YKELVG 70
>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 = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 88 GQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145
Q ++ T+ Q+Q LE F+ + + ++A L +V +WF+NRRA+ R
Sbjct: 2 SQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWR 59
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
Length = 67
Score = 27.3 bits (59), Expect = 5.5, Method: Composition-based stats.
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 117 ERKVQLAKELGLQPRQVAIWFQNRRAR 143
E+K QLA++ GL QV WF N R R
Sbjct: 29 EQKKQLAQDTGLTILQVNNWFINARRR 55
>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 = 5.9, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 120 VQLAKELGLQPRQVAIWFQNRRARSR 145
+A +LGL+ V +WF NRR + +
Sbjct: 127 THIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 27.3 bits (59), Expect = 6.0, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 99 TQVQFLER--NFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLG 150
T++ F +R + + EN+LE E KV+L GL P R R + Q+LG
Sbjct: 1025 TRLSFYKRIASAKTENELE-EIKVELIDRFGLLPDPARTLLDIARLRQQAQKLG 1077
>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 = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 117 ERKVQLAKELGLQPRQVAIWFQNRRAR 143
E K +LA++ G+ QV+ WF N+R R
Sbjct: 32 EAKEELARKCGITVSQVSNWFGNKRIR 58
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
0.315 0.130 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,088,476
Number of Sequences: 62578
Number of extensions: 183035
Number of successful extensions: 489
Number of sequences better than 100.0: 94
Number of HSP's better than 100.0 without gapping: 85
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 404
Number of HSP's gapped (non-prelim): 94
length of query: 206
length of database: 14,973,337
effective HSP length: 94
effective length of query: 112
effective length of database: 9,091,005
effective search space: 1018192560
effective search space used: 1018192560
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)