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= 004294
(763 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 88 PNKKKRYHR--HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 145
P +K+R +R T Q++E+E F +PD R+EL+ ++GL +++ WFQN+R +
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61
Query: 146 KTQHE 150
+ Q +
Sbjct: 62 RKQEK 66
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
++KR +Q Q+ E+E FK+ + +R+ L+ + L P QVK WFQN R +MK Q
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 33/53 (62%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQHE 150
T Q++E+E F +PD R+EL+ ++GL +++ WFQN+R + + Q +
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>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 = 46.2 bits (108), Expect = 7e-05, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 83 DQEQRP----NKKKRYHRHT--QHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKF 136
D E P +K+R R T Q+ E+E F+ +PD R+EL++ L +++
Sbjct: 5 DCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV 64
Query: 137 WFQNKRTQMKTQH 149
WFQN+R +++ QH
Sbjct: 65 WFQNRRARLRKQH 77
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 46.2 bits (108), Expect = 8e-05, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 32/51 (62%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
T Q++E+E F +PD R+EL+ ++GL +++ WFQN+R + + Q
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 85 EQRPNKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQ 144
E+RP + Q+ ++ F E + +++R++LS ELGL Q+K WFQNKR +
Sbjct: 3 EKRPRTA-----FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
Query: 145 MK 146
+K
Sbjct: 58 IK 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 85 EQRPNKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQ 144
E+RP + Q+ ++ F E + +++R++LS ELGL Q+K WFQNKR +
Sbjct: 1 EKRPRTA-----FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 55
Query: 145 MK 146
+K
Sbjct: 56 IK 57
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 87 RPNKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
R +KKR +T+HQ E+E F + +R E++R L L QVK WFQN+R +MK
Sbjct: 11 RSTRKKRC-PYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>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 = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 37/74 (50%)
Query: 88 PNKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKT 147
P +KK T+ Q+ E+E F + + +R L+R L + QVK WFQN+RT+ +
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
Query: 148 QHERHENTQLRTEN 161
Q + + N
Sbjct: 75 QTAEEREAERQAAN 88
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 91 KKRYHR--HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
KKR +R T +Q++E+E F++ +PD R++L+ L +V+ WFQN+R + + +
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWR-K 66
Query: 149 HERHENTQ 156
ER Q
Sbjct: 67 RERFGQMQ 74
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 33/56 (58%)
Query: 99 QHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQHERHEN 154
HQ++ M+++F +PD K K+L+++ GL ++ WFQN R + + R EN
Sbjct: 16 HHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQEN 71
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 12/77 (15%)
Query: 88 PNKK-KRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
PNKK KR T+ Q E+E F++ + +R+ L+ + L P QVK WFQN R + K
Sbjct: 9 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTK 68
Query: 147 TQHERHENTQLRTENEK 163
R +NEK
Sbjct: 69 -----------RAQNEK 74
>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 = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 12/77 (15%)
Query: 88 PNKK-KRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
PNKK KR T+ Q E+E F++ + +R+ L+ + L P QVK WFQN R + K
Sbjct: 6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTK 65
Query: 147 TQHERHENTQLRTENEK 163
R +NEK
Sbjct: 66 -----------RAQNEK 71
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 43.9 bits (102), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 85 EQRPNKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQ 144
E+RP + Q+ ++ F E + +++R++LS ELGL Q+K WF+NKR +
Sbjct: 3 EKRPRTA-----FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAK 57
Query: 145 MK 146
+K
Sbjct: 58 IK 59
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 18/38 (47%), Positives = 27/38 (71%)
Query: 109 FKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
F E + +++R++LS ELGL Q+K WFQNKR ++K
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 5/62 (8%)
Query: 85 EQRPNKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQ 144
E+RP + Q+ ++ F E + +++R++LS ELGL Q+K WFQN+R +
Sbjct: 1 EKRPRTA-----FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAK 55
Query: 145 MK 146
+K
Sbjct: 56 IK 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 43.5 bits (101), Expect = 5e-04, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 31/48 (64%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 145
+ Q+ ++ F E + +++R++LS ELGL Q+K WFQNKR ++
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>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 = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 85 EQRPNKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQ 144
E+RP + Q+ ++ F E + +++R++LS ELGL Q+K WFQN R +
Sbjct: 1 EKRPRTA-----FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 55
Query: 145 MK 146
+K
Sbjct: 56 IK 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 = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 7/72 (9%)
Query: 79 ASGDDQEQRPNKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWF 138
A+G+ + QR + +T++Q E+E F + ++R E++ L L Q+K WF
Sbjct: 24 ANGETKRQRTS-------YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWF 76
Query: 139 QNKRTQMKTQHE 150
QN+R + K +H+
Sbjct: 77 QNRRMKWKKEHK 88
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 35/56 (62%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQHERHE 153
TQ+QI+ +E F+ +P ++L+++L LE +++ WFQN+R ++K H +
Sbjct: 9 TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ 64
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+ Q+ ++ F E + +++R++LS ELGL Q+K WF NKR ++K
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 42.7 bits (99), Expect = 8e-04, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 89 NKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
++K+ + Q+ + F E + +++R++LS ELGL Q+K WFQNKR +++
Sbjct: 2 DEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 33/56 (58%)
Query: 91 KKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+K+ +T++Q E+E F + +R E++R L L QVK WFQN+R +MK
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 93 RYHR--HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
R HR T Q++ +E F+E +PD R++L+R++ L +V+ WF+N+R + +
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQHERHEN 154
T QI E+E F + + + +LS +L L QVK WF+N+R + K Q ++H++
Sbjct: 10 TSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKD 66
>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 = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQH 149
+++R H T Q+QE+EA F+ +PD R+E++ L +V+ WF+N+R + + +
Sbjct: 4 RRQRTH-FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 150 E 150
E
Sbjct: 63 E 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 34/59 (57%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
+++ +T++Q E+E F + ++R E++ L L Q+K WFQN+R ++K +
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
K+KR T I+ + A+F++ P P ++ E ++EL + V+ WF N+R +K
Sbjct: 93 KRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQTLK 149
>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 = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 29/49 (59%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+Q Q+ E+E FK+ + +R +L+ L L QVK WFQN+R + K
Sbjct: 10 SQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 89 NKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
++K+ + Q+ ++ F E + +++R++LS ELGL QVK WF+N R ++K
Sbjct: 3 DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 97 HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
++ Q+ ++ F++ + +R EL+ LGL QVK WFQNKR+++K
Sbjct: 14 YSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQH 149
+++R H T Q+QE+EA F+ +PD R+E++ L +V+ WF+N+R + + +
Sbjct: 4 RRQRTH-FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 150 E 150
E
Sbjct: 63 E 63
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 34/60 (56%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQH 149
+K+ +T++Q E+E F + ++R E++ L L Q+K WFQN+R + K ++
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 62
>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 = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 35/61 (57%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQH 149
+K+ +T++Q E+E F + ++R E++ L L Q+K WFQN+R + K ++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 150 E 150
+
Sbjct: 62 K 62
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
T Q++E+E F+ +PD R+EL++ L +V+ WF N+R + + Q
Sbjct: 10 TAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 3/68 (4%)
Query: 83 DQEQRPNKKKRYHRHTQHQIQEMEAFFK---ECPHPDDKQRKELSRELGLEPLQVKFWFQ 139
D + K R HR T+ ++ +E++F E P+ D K + L + L +Q+K W
Sbjct: 20 DMINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVS 79
Query: 140 NKRTQMKT 147
N+R + KT
Sbjct: 80 NRRRKEKT 87
>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 = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 35/61 (57%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQH 149
+K+ +T++Q E+E F + ++R E++ L L Q+K WFQN+R + K ++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61
Query: 150 E 150
+
Sbjct: 62 K 62
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 91 KKRYHRHTQHQIQ-EMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+KR +++++ +E F +CP P +Q ++ +LGLE V+ WF N+R + K
Sbjct: 8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 90 KKKRYHR--HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
KK R R T+ Q+ +E F++ + R +L+ LGL LQVK W+QN+R + K
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi
Tarazu Homeodomain From Drosophila And Comparison With
The Antennapedia Homeodomain
Length = 70
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 89 NKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
+ K+ +T++Q E+E F + ++R +++ L L Q+K WFQN+R MK++
Sbjct: 2 DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRR--MKSK 59
Query: 149 HER 151
+R
Sbjct: 60 KDR 62
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 105 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+E F+ + K+++E++++ G+ PLQV+ WF NKR + K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 32/54 (59%)
Query: 97 HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQHE 150
+T++Q E+E F + ++R E++ L L Q+K WFQN+R + K +++
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 88 PNKKKRYHR--HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 145
P K R R T Q+ E+E F + +R +++ L L +QVK WFQN+R +
Sbjct: 3 PGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKW 62
Query: 146 K 146
K
Sbjct: 63 K 63
>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 = 0.013, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 105 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+E F+ + K+++E++++ G+ PLQV+ WF NKR + K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 105 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+E F+ + K+++E++++ G+ PLQV+ WF NKR + K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 92 KRYHRHTQHQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+R R+ Q E+ E F+ P+P ++ ++EL+R+ G+ QV WF NKR + K
Sbjct: 2 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 90 KKKRYHRHTQHQIQEMEAFFK---ECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
K R HR T+ ++ +E++F E P+ D K + L + L +Q+K W N+R + K
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 61
Query: 147 T 147
T
Sbjct: 62 T 62
>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 = 38.1 bits (87), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 105 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+E F+ + K+++E++++ G+ PLQV+ WF NKR + K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 37.7 bits (86), Expect = 0.026, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 93 RYHRHTQHQIQEMEAFFK---ECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKT 147
R HR T+ ++ +E++F E P+ D K + L + L +Q+K W N+R + KT
Sbjct: 1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 37.7 bits (86), Expect = 0.027, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
T Q+ +E F++ + +R E S L L QVK WFQN+R + K
Sbjct: 8 TTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 37.7 bits (86), Expect = 0.027, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 96 RHTQHQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
RH Q E+ E F+ P+P ++ ++EL+++ G+ QV WF NKR + K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>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 = 37.4 bits (85), Expect = 0.032, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 99 QHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
+ Q+ + + P PD +++L GL P ++ WFQNKR + K +
Sbjct: 12 EKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
>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 = 37.4 bits (85), Expect = 0.033, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 27/53 (50%)
Query: 101 QIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQHERHE 153
Q+ E+E F + +R L++ L L QVK WFQN+R + K + E
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 37.4 bits (85), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 31/50 (62%)
Query: 97 HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
T+ Q+ +EA F + +PD R+E++ ++ L +V+ WF+N+R + +
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 37.4 bits (85), Expect = 0.035, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 96 RHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
R T +Q++ ++ FF +P D + ++LS L L + WFQN R + +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 37.0 bits (84), Expect = 0.040, Method: Composition-based stats.
Identities = 25/96 (26%), Positives = 49/96 (51%), Gaps = 5/96 (5%)
Query: 54 SESEIARLRE--EEFDSTKSGSENHEGASGDDQEQRPNKKKRYHRHTQHQIQ-EMEAFFK 110
S +++LR E++ +EN + S + + K+KR +++++ +E F
Sbjct: 59 SLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRKR--TSIENRVRWSLETMFL 116
Query: 111 ECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+ P P +Q ++ +LGLE V+ WF N+R + K
Sbjct: 117 KSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 37.0 bits (84), Expect = 0.042, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 92 KRYHRHTQHQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+R R+ Q E+ E F+ P+P ++ ++EL+++ G+ QV WF NKR + K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>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 = 37.0 bits (84), Expect = 0.045, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 24/33 (72%)
Query: 113 PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 145
P+P ++Q+K+L+++ GL LQV WF N R ++
Sbjct: 24 PYPSEEQKKQLAQDTGLTILQVNNWFINARRRI 56
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 36.6 bits (83), Expect = 0.053, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 29/51 (56%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
++ Q+ E+E F + +R L++ L + QVK WFQN+RT+ + Q
Sbjct: 5 SRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 0.057, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 96 RHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
R + Q E+E F+ + +RK L++ L L QVK WFQN+R + +
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 36.2 bits (82), Expect = 0.066, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 92 KRYHRHTQHQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+R R+ Q E+ E F+ P+P ++ ++EL+++ G+ QV WF NKR + K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>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 = 35.8 bits (81), Expect = 0.088, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 89 NKKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
NK+ R +T+ Q+ E+E F + +R EL+ L L +K WFQN+R + K +
Sbjct: 3 NKRTRT-AYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
Query: 149 HE 150
+
Sbjct: 62 ED 63
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 35.8 bits (81), Expect = 0.092, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 92 KRYHRHTQHQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+R R+ Q E+ E F+ P+P ++ ++EL+++ G+ QV WF NKR + K
Sbjct: 3 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>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 = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
K+K +Q Q+ ++ F++ + +Q +ELS L L QVK WFQN+R + K
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 31/53 (58%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQHE 150
TQ QI+ +E F+ +PD R+ L+ ++ L +++ WF N+R + + + +
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
>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 = 33.9 bits (76), Expect = 0.34, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 92 KRYHR-HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQ 148
+RY T+ Q+ +E F + + +R EL+ +L L +K WFQN+R + K Q
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 33.9 bits (76), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 105 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQ 144
+ ++ P+P ++++EL+ GL QV WF+N+R +
Sbjct: 509 LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 33.9 bits (76), Expect = 0.38, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 55 ESEIARLREEEFDSTKSGSENHEGASGDDQEQRPNKKKRYHRHTQHQIQEMEAFFKECPH 114
E E R+ + K + H G D+ P K + T Q + + A FKE
Sbjct: 68 EPEFQRMSALRLAACKRKEQEH----GKDRGNTPKKPRLVF--TDVQRRTLHAIFKENKR 121
Query: 115 PDDKQRKELSRELGLEPLQVKFWFQNKR 142
P + + +S++LGLE V +F N R
Sbjct: 122 PSKELQITISQQLGLELSTVSNFFMNAR 149
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 33.9 bits (76), Expect = 0.39, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 55 ESEIARLREEEFDSTKSGSENHEGASGDDQEQRPNKKKRYHRHTQHQIQEMEAFFKECPH 114
E E R+ + K + H G D+ P K + T Q + + A FKE
Sbjct: 66 EPEFQRMSALRLAACKRKEQEH----GKDRGNTPKKPRLVF--TDVQRRTLHAIFKENKR 119
Query: 115 PDDKQRKELSRELGLEPLQVKFWFQNKR 142
P + + +S++LGLE V +F N R
Sbjct: 120 PSKELQITISQQLGLELSTVSNFFMNAR 147
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 33.5 bits (75), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 27/52 (51%)
Query: 98 TQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQH 149
T Q+ E+E F + +R E++ L L QVK WFQN+R + K +
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE 93
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 33.5 bits (75), Expect = 0.48, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+KKR +T+ Q++E+E + +R+ +S L QV WFQN+R + K
Sbjct: 2 RKKRV-PYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 33.1 bits (74), Expect = 0.53, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 90 KKKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+KKR +T+ Q++E+E + +R+ +S L QV WFQN+R + K
Sbjct: 8 RKKRV-PYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
Length = 66
Score = 33.1 bits (74), Expect = 0.65, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 96 RHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKR 142
+ T+ QI ++A F + PDD + L GL ++K WF + R
Sbjct: 10 KKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHR 56
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 32.7 bits (73), Expect = 0.86, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 77 EGASGDDQEQRPNKKKRYHR-HTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVK 135
E + +++ P KK++ + Q+ + F+ + +Q +ELS L L QVK
Sbjct: 8 ENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVK 67
Query: 136 FWFQNKRTQMK 146
WFQN+R + K
Sbjct: 68 TWFQNQRMKSK 78
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 32.3 bits (72), Expect = 0.92, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 89 NKKKRYHRHTQHQIQE--MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
N++KR R T + +E F E P ++ ++ EL LE V+ WF N+R + K
Sbjct: 84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1BMO|A Chain A, Bm-40, FsEC DOMAIN PAIR
pdb|1BMO|B Chain B, Bm-40, FsEC DOMAIN PAIR
Length = 233
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 123 LSRELGLEPLQVKFWFQNKRTQMKTQHERHENTQLRTENEKLRADNMRYRE 173
L EL PL+++ W +N + T +ER E+ L TE +KLR + E
Sbjct: 86 LDSELTEFPLRMRDWLKN---VLVTLYERDEDNNLLTEKQKLRVKKIHENE 133
>pdb|1NUB|A Chain A, Helix C Deletion Mutant Of Bm-40 Fs-Ec Domain Pair
pdb|1NUB|B Chain B, Helix C Deletion Mutant Of Bm-40 Fs-Ec Domain Pair
Length = 229
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 123 LSRELGLEPLQVKFWFQNKRTQMKTQHERHENTQLRTENEKLRADNMRYRE 173
L EL PL+++ W +N + T +ER E+ L TE +KLR + E
Sbjct: 90 LDSELTEFPLRMRDWLKN---VLVTLYERDEDNNLLTEKQKLRVKKIHENE 137
>pdb|1SRA|A Chain A, Structure Of A Novel Extracellular Ca2+-Binding Module In
Bm-40(Slash)sparc(Slash)osteonectin
Length = 151
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 123 LSRELGLEPLQVKFWFQNKRTQMKTQHERHENTQLRTENEKLRADNMRYRE 173
L EL PL+++ W +N + T +ER E+ L TE +KLR + E
Sbjct: 4 LDSELTEFPLRMRDWLKN---VLVTLYERDEDNNLLTEKQKLRVKKIHENE 51
>pdb|2V53|A Chain A, Crystal Structure Of A Sparc-Collagen Complex
Length = 230
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 123 LSRELGLEPLQVKFWFQNKRTQMKTQHERHENTQLRTENEKLRADNMRYRE 173
L EL PL+++ W +N + T +ER E+ L TE +KLR + E
Sbjct: 91 LDSELTEFPLRMRDWLKN---VLVTLYERDEDNNLLTEKQKLRVKKIHENE 138
>pdb|2OOX|A Chain A, Crystal Structure Of The Adenylate Sensor From
Amp-activated Protein Kinase Complexed With Amp
pdb|2OOX|C Chain C, Crystal Structure Of The Adenylate Sensor From
Amp-activated Protein Kinase Complexed With Amp
pdb|2OOY|A Chain A, Crystal Structure Of The Adenylate Sensor From Amp-
Activated Protein Kinase Complexed With Atp
pdb|2OOY|C Chain C, Crystal Structure Of The Adenylate Sensor From Amp-
Activated Protein Kinase Complexed With Atp
pdb|2QR1|A Chain A, Crystal Structure Of The Adenylate Sensor From
Amp-Activated Protein Kinase In Complex With Adp
pdb|2QR1|C Chain C, Crystal Structure Of The Adenylate Sensor From
Amp-Activated Protein Kinase In Complex With Adp
pdb|2QRC|A Chain A, Crystal Structure Of The Adenylate Sensor From
Amp-Activated Protein Kinase In Complex With Adp And Amp
pdb|2QRC|C Chain C, Crystal Structure Of The Adenylate Sensor From
Amp-Activated Protein Kinase In Complex With Adp And Amp
pdb|2QRD|A Chain A, Crystal Structure Of The Adenylate Sensor From
Amp-Activated Protein Kinase In Complex With Adp And Atp
pdb|2QRD|C Chain C, Crystal Structure Of The Adenylate Sensor From
Amp-Activated Protein Kinase In Complex With Adp And Atp
pdb|2QRE|A Chain A, Crystal Structure Of The Adenylate Sensor From
Amp-Activated Protein Kinase In Complex With
5-Aminoimidazole-4-Carboxamide 1-Beta-D- Ribofuranotide
(Zmp)
pdb|2QRE|C Chain C, Crystal Structure Of The Adenylate Sensor From
Amp-Activated Protein Kinase In Complex With
5-Aminoimidazole-4-Carboxamide 1-Beta-D- Ribofuranotide
(Zmp)
Length = 137
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 44/98 (44%), Gaps = 23/98 (23%)
Query: 388 ALQVMTAEFQVPSP--------LVPTRESYYVRYCKQHGEGTWAVVDVSLDNLRPSPAVR 439
ALQ A+F VP P + + + + +CK+ G+ T+A +++ L + P
Sbjct: 33 ALQRAGAQFTVPKPVNGKYRSDMYTIKSRWEIPHCKREGKNTYAYIELQLYEVMP----- 87
Query: 440 CRRRPSGCLIQEMP-NGYSKVTWVEHVE-VDDRGVHNL 475
GC + ++ NGY + H E D G+ +L
Sbjct: 88 ------GCFMLDVKSNGYKDI--YSHPERTADHGMDDL 117
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 25/41 (60%)
Query: 106 EAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+ F +PD+K+ K LS++L +++ WF+++R Q K
Sbjct: 25 KVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 105 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+E+ F +CP P + L+ L LE V+ WF N+R + K
Sbjct: 114 LESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 31.6 bits (70), Expect = 1.9, Method: Composition-based stats.
Identities = 14/56 (25%), Positives = 30/56 (53%)
Query: 91 KKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
+K+ +++ Q++E+E + +R+++S L Q+ WFQN+R + K
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 31.2 bits (69), Expect = 2.5, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 114 HPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 146
HPD+K+ + LS++L + ++ WF+ +R Q K
Sbjct: 25 HPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 91 KKRYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQN 140
K+ R T Q++ + +F P ++Q KE++ + GL +K WF+N
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 29.6 bits (65), Expect = 5.9, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 113 PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 145
P+P + ++K+++ + L LQV WF N R ++
Sbjct: 33 PYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 29.3 bits (64), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 12/57 (21%), Positives = 27/57 (47%)
Query: 93 RYHRHTQHQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKTQH 149
+Y Q++ +E+ F + P P D++ L E + ++ WF +R ++ +
Sbjct: 10 KYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE 66
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
0.316 0.131 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,096,045
Number of Sequences: 62578
Number of extensions: 896664
Number of successful extensions: 2139
Number of sequences better than 100.0: 89
Number of HSP's better than 100.0 without gapping: 82
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2057
Number of HSP's gapped (non-prelim): 89
length of query: 763
length of database: 14,973,337
effective HSP length: 106
effective length of query: 657
effective length of database: 8,340,069
effective search space: 5479425333
effective search space used: 5479425333
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: 55 (25.8 bits)