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= 045292
(673 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 35/59 (59%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
+RKR +Q Q+ E+E FK+ + +R+ L+ + L P QVK WFQN R +MK Q
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 57 PKRK-RYHR--HTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 113
PKRK R +R T Q++E+E F +PD R+EL+ ++GL +++ WFQN+R +
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61
Query: 114 KAQHE 118
+ Q +
Sbjct: 62 RKQEK 66
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
+R+R H T +Q+QE+EA F+ +PD R+E++ L +V+ WF+N+R + + +
Sbjct: 4 RRQRTH-FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 118 E 118
E
Sbjct: 63 E 63
>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 = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
+R+R H T +Q+QE+EA F+ +PD R+E++ L +V+ WF+N+R + + +
Sbjct: 4 RRQRTH-FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 118 E 118
E
Sbjct: 63 E 63
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 33/53 (62%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQHE 118
T Q++E+E F +PD R+EL+ ++GL +++ WFQN+R + + Q +
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK-AQ 116
KRKR T+ Q E+E F++ + +R+ L+ + L P QVK WFQN R + K AQ
Sbjct: 12 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
Query: 117 HER 119
+E+
Sbjct: 72 NEK 74
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 32/51 (62%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
T Q++E+E F +PD R+EL+ ++GL +++ WFQN+R + + Q
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK-AQ 116
KRKR T+ Q E+E F++ + +R+ L+ + L P QVK WFQN R + K AQ
Sbjct: 9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
Query: 117 HER 119
+E+
Sbjct: 69 NEK 71
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 32/49 (65%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ Q+ ++ F E + +++R++LS ELGL Q+K WFQNKR ++K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 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 = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 32/49 (65%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ Q+ ++ F E + +++R++LS ELGL Q+K WFQNKR ++K
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 57 PKRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
P+R R T QI E+E F + + + +LS +L L QVK WF+N+R + K Q
Sbjct: 2 PRRTRT-TFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
Query: 117 HERHENQ 123
++H++Q
Sbjct: 61 SDQHKDQ 67
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 69 QIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
Q+ E+E F+ +PD R+EL++ L +++ WFQN+R +++ QH
Sbjct: 29 QLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
>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: 77 FKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
F E + +++R++LS ELGL Q+K WFQNKR ++K
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>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 = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 32/49 (65%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ Q+ ++ F E + +++R++LS ELGL Q+K WF+NKR ++K
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 32/49 (65%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ Q+ ++ F E + +++R++LS ELGL Q+K WFQN+R ++K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 31/48 (64%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 113
+ Q+ ++ F E + +++R++LS ELGL Q+K WFQNKR ++
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>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 = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 52 DPSQHPKRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRT 111
+PS+ KRKR T + I+ + A+F++ P P ++ E ++EL + V+ WF N+R
Sbjct: 89 EPSK--KRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQ 146
Query: 112 QMK 114
+K
Sbjct: 147 TLK 149
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQHERHENQIL 125
TQ QI+ +E F+ +P ++L+++L LE +++ WFQN+R ++K H E+Q L
Sbjct: 9 TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR--ESQFL 66
>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 = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ Q+ ++ F E + +++R++LS ELGL Q+K WFQN R ++K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>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 = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ Q+ ++ F E + +++R++LS ELGL Q+K WF NKR ++K
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>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 = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 57 PKRKRYHRHTQR-QIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKA 115
PKRK+ R Q+ E+E F + + +R L+R L + QVK WFQN+RT+ +
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
Query: 116 QHERHENQILKAENQ 130
Q +A N+
Sbjct: 75 QTAEEREAERQAANR 89
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 34/59 (57%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
KR+ T Q++E+E F++ +PD R++L+ L +V+ WFQN+R + + +
Sbjct: 9 KRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ Q+ + F E + +++R++LS ELGL Q+K WFQNKR +++
Sbjct: 11 SSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 32/56 (57%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RK+ +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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 61 RYHR--HTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
R HR T Q++ +E F+E +PD R++L+R++ L +V+ WF+N+R + +
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 32/56 (57%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RK+ +T+ Q E+E F + +R E++R L L QVK WFQN+R +MK
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
+R+ +T+ Q E+E F + ++R E++ L L Q+K WFQN+R ++K +
Sbjct: 20 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>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 = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
KR+R +T+ Q E+E F + ++R E++ L L Q+K WFQN+R + K +H
Sbjct: 29 KRQRT-SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH 87
Query: 118 E 118
+
Sbjct: 88 K 88
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
+R+ T Q++E+E F+ +PD R+EL++ L +V+ WF N+R + + Q
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>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 = 0.003, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+RK +Q Q+ E+E FK+ + +R +L+ L L QVK WFQN+R + K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 0.003, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 52 DPSQHPKRKRYHR--HTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNK 109
+P K+ R R T+ Q+ +E F++ + R +L+ LGL LQVK W+QN+
Sbjct: 9 EPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNR 68
Query: 110 RTQMK 114
R + K
Sbjct: 69 RMKWK 73
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 32/54 (59%)
Query: 69 QIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQHERHEN 122
Q++ M+++F +PD K K+L+++ GL ++ WFQN R + + R EN
Sbjct: 18 QLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQEN 71
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 33/56 (58%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RK ++ Q+ ++ F++ + +R EL+ LGL QVK WFQNKR+++K
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 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 = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 31/49 (63%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ Q+ ++ F E + +++R++LS ELGL QVK WF+N R ++K
Sbjct: 12 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
R+R T Q+ E+E F + +R +++ L L +QVK WFQN+R + K
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>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 = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 60 KRYHRHTQRQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+R R+ +Q E+ E F+ P+P ++ ++EL+R+ G+ QV WF NKR + K
Sbjct: 2 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 64 RHTQRQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RH +Q E+ E F+ P+P ++ ++EL+++ G+ QV WF NKR + K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 38.5 bits (88), Expect = 0.013, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 73 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+E F+ + K+++E++++ G+ PLQV+ WF NKR + K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 67 QRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
++Q+ + + P PD +++L GL P ++ WFQNKR + K +
Sbjct: 12 EKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 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 = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 73 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+E F+ + K+++E++++ G+ PLQV+ WF NKR + K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1YRN|A Chain A, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1F43|A Chain A, Solution Structure Of The Mata1 Homeodomain
Length = 61
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 73 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+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 = 38.1 bits (87), Expect = 0.018, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 73 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+E F+ + K+++E++++ G+ PLQV+ WF NKR + K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 37.7 bits (86), Expect = 0.019, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 58 KRKRYHR-HTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
+RKR + +T+ Q E+E F + ++R E++ L L Q+K WFQN+R + K +
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
Query: 117 H 117
+
Sbjct: 62 N 62
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 37.7 bits (86), Expect = 0.019, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 60 KRYHRHTQRQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+R R+ +Q E+ E F+ P+P ++ ++EL+++ G+ QV WF NKR + K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 37.7 bits (86), Expect = 0.021, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 59 RKRYHRHTQRQIQ-EMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RKR + +++ +E F + P P +Q ++ +LGLE V+ WF N+R + K
Sbjct: 96 RKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 37.7 bits (86), Expect = 0.021, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 28/56 (50%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RK T Q+ +E F++ + +R E S L L QVK WFQN+R + K
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>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 = 37.7 bits (86), Expect = 0.022, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
KR R +T+ Q E+E F + ++R E++ L L Q+K WFQN+R + K ++
Sbjct: 3 KRGR-QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 118 E 118
+
Sbjct: 62 K 62
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 37.7 bits (86), Expect = 0.022, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 60 KRYHRHTQRQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+R R+ +Q E+ E F+ P+P ++ ++EL+++ G+ QV WF NKR + K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>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 = 37.0 bits (84), Expect = 0.032, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 27/53 (50%)
Query: 69 QIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQHERHE 121
Q+ E+E F + +R L++ L L QVK WFQN+R + K + E
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67
>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 = 37.0 bits (84), Expect = 0.032, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 65 HTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQHE 118
+T+ Q E+E F + ++R E++ L L Q+K WFQN+R + K +++
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 37.0 bits (84), Expect = 0.033, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 4/59 (6%)
Query: 60 KRYHRHTQRQIQEM--EAFFKEC--PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+R R+ +Q E+ E F+ P+P ++ ++EL+++ G+ QV WF NKR + K
Sbjct: 3 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>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 = 37.0 bits (84), Expect = 0.036, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
KR R +T+ Q E+E F + ++R E++ L L Q+K WFQN+R + K ++
Sbjct: 3 KRGR-QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61
Query: 118 E 118
+
Sbjct: 62 K 62
>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 = 0.040, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 24/33 (72%)
Query: 81 PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 113
P+P ++Q+K+L+++ GL LQV WF N R ++
Sbjct: 24 PYPSEEQKKQLAQDTGLTILQVNNWFINARRRI 56
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 37.0 bits (84), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 38/64 (59%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQHE 118
R+ T+ Q+ +EA F + +PD R+E++ ++ L +V+ WF+N+R + + Q +
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67
Query: 119 RHEN 122
+ +N
Sbjct: 68 QQQN 71
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 36.2 bits (82), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 73 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+E F +CP P +Q ++ +LGLE V+ WF N+R + K
Sbjct: 23 LETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 36.2 bits (82), Expect = 0.057, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 29/51 (56%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
++ Q+ E+E F + +R L++ L + QVK WFQN+RT+ + Q
Sbjct: 5 SRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 35.8 bits (81), Expect = 0.071, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
KR R +T+ Q E+E F + ++R +++ L L Q+K WFQN+R MK++
Sbjct: 4 KRTR-QTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRR--MKSKK 60
Query: 118 ER 119
+R
Sbjct: 61 DR 62
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 35.8 bits (81), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
T RQ+ E+E F + +R E++ L L QVK WFQN+R + K +
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRE 93
>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 = 35.8 bits (81), Expect = 0.074, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 58 KRKRYHRHTQRQIQEMEAFFK---ECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
K R HR T+ ++ +E++F E P+ D K + L + L +Q+K W N+R + K
Sbjct: 27 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86
>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 = 35.8 bits (81), Expect = 0.079, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 61 RYHRHTQRQIQEMEAFFK---ECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
R HR T+ ++ +E++F E P+ D K + L + L +Q+K W N+R + K
Sbjct: 1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 57
>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 = 35.8 bits (81), Expect = 0.084, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 58 KRKRYHRHTQRQIQEMEAFFK---ECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
K R HR T+ ++ +E++F E P+ D K + L + L +Q+K W N+R + K
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 61
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%)
Query: 64 RHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
R T Q++ ++ FF +P D + ++LS L L + WFQN R + +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RK+ +T+ Q++E+E + +R+ +S L QV WFQN+R + K
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 29/56 (51%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RK+ +T+ Q++E+E + +R+ +S L QV WFQN+R + K
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>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 = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
K+K +Q Q+ ++ F++ + +Q +ELS L L QVK WFQN+R + K
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 73 MEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKA 115
+ ++ P+P ++++EL+ GL QV WF+N+R + +A
Sbjct: 509 LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRA 551
>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 = 34.7 bits (78), Expect = 0.16, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
KR R +T+ Q+ E+E F + +R EL+ L L +K WFQN+R + K +
Sbjct: 4 KRTRT-AYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
Query: 118 E 118
+
Sbjct: 63 D 63
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 66 TQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQHERHENQ 123
TQ QI+ +E F+ +PD R+ L+ ++ L +++ WF N+R + + + E+ NQ
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR-REEKLRNQ 71
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 33.5 bits (75), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%)
Query: 45 APSGDDQDPSQHPKRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKF 104
+P+ D+ +Q KRK+ +E+ F +CP P + L+ L LE V+
Sbjct: 86 SPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRV 145
Query: 105 WFQNKRTQMK 114
WF N+R + K
Sbjct: 146 WFCNRRQKEK 155
>pdb|2JTD|A Chain A, Skelemin Immunoglobulin C2 Like Domain 4
Length = 142
Score = 33.5 bits (75), Expect = 0.41, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 65 HTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKR--TQMKAQHERHEN 122
H + +++ + A +E P + EL+ E+ LE QV+FW Q ++ + K + +E
Sbjct: 19 HMEEEMKRLLALSQEHKFPTVPTKSELAVEI-LEKGQVRFWMQAEKLSSNAKVSYIFNEK 77
Query: 123 QILKAENQKLRAENN 137
+I + K+ + N
Sbjct: 78 EIFEGPKYKMHIDRN 92
>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 = 33.1 bits (74), Expect = 0.53, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 60 KRYHR-HTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQ 116
+RY T+ Q+ +E F + + +R EL+ +L L +K WFQN+R + K Q
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|2X2S|A Chain A, Crystal Structure Of Sclerotinia Sclerotiorum Agglutinin
Ssa
pdb|2X2S|B Chain B, Crystal Structure Of Sclerotinia Sclerotiorum Agglutinin
Ssa
pdb|2X2S|C Chain C, Crystal Structure Of Sclerotinia Sclerotiorum Agglutinin
Ssa
pdb|2X2S|D Chain D, Crystal Structure Of Sclerotinia Sclerotiorum Agglutinin
Ssa
pdb|2X2T|A Chain A, Crystal Structure Of Sclerotinia Sclerotiorum Agglutinin
Ssa In Complex With Gal-Beta1,3-Galnac
Length = 153
Score = 32.7 bits (73), Expect = 0.61, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 3 QPNTFESHHMFDMTRRSSESDLGKLKEDDYETKSGTETMEMEAPSGDDQ 51
+P T + +F + + SE LG+L DY T SG + + A + D+Q
Sbjct: 100 KPATTHQYEVFTINNKVSE--LGQLTVKDYSTHSGADVLSASAKTADNQ 146
>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 = 32.7 bits (73), Expect = 0.63, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 64 RHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKR 110
+ T+ QI ++A F + PDD + L GL ++K WF + R
Sbjct: 10 KKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHR 56
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 32.7 bits (73), Expect = 0.73, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 27/57 (47%)
Query: 58 KRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
KRKR + +E F E P ++ ++ EL LE V+ WF N+R + K
Sbjct: 87 KRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 32.3 bits (72), Expect = 0.81, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 59 RKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
RK+ +++ Q++E+E + +R+++S L Q+ WFQN+R + K
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%)
Query: 64 RHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
R + Q E+E F+ + +RK L++ L L QVK WFQN+R + +
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 2/75 (2%)
Query: 40 TMEMEAPSGDDQDPSQHPKRKRYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEP 99
+ E +D+ P + K + TQ + + F+ + +Q +ELS L L
Sbjct: 6 SAENSVAKKEDKVPVKKQKTRTVFSSTQLCV--LNDRFQRQKYLSLQQMQELSNILNLSY 63
Query: 100 LQVKFWFQNKRTQMK 114
QVK WFQN+R + K
Sbjct: 64 KQVKTWFQNQRMKSK 78
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 25/41 (60%)
Query: 74 EAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
+ F +PD+K+ K LS++L +++ WF+++R Q K
Sbjct: 25 KVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 82 HPDDKQRKELSRELGLEPLQVKFWFQNKRTQMK 114
HPD+K+ + LS++L + ++ WF+ +R Q K
Sbjct: 25 HPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>pdb|2HZQ|A Chain A, Crystal Structure Of Human Apolipoprotein D (Apod) In
Complex With Progesterone
pdb|2HZR|A Chain A, Crystal Structure Of Human Apolipoprotein D (Apod)
Length = 174
Score = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 5/86 (5%)
Query: 79 ECPHPDDKQRKELSRELG--LEPLQVKFWFQNKRTQMKAQHERHENQILKAENQKLRAEN 136
+CP+P ++ ++++ G E ++ F+N R ++A + EN +K NQ+LRA+
Sbjct: 5 KCPNPPVQENFDVNKYPGRWYEIEKIPTTFENGRC-IQANYSLXENGKIKVLNQELRADG 63
Query: 137 NRYKEALGNATCPNCGGPAALGEMSF 162
+ G AT N PA L E+ F
Sbjct: 64 T-VNQIEGEATPVNLTEPAKL-EVKF 87
>pdb|2RPB|A Chain A, The Solution Structure Of Membrane Protein
Length = 113
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 16/30 (53%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 155 AALGEMSFDE--QHLRIENARLREEIDRIS 182
A +GEM DE I NARLREE+D+I+
Sbjct: 64 AIIGEMELDETLSGRDIINARLREELDKIT 93
>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 = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 28/57 (49%)
Query: 61 RYHRHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQH 117
+Y Q++ +E+ F + P P D++ L E + ++ WF +R ++ A+
Sbjct: 10 KYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEE 66
>pdb|3NAP|A Chain A, Structure Of Triatoma Virus (Trv)
Length = 271
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 12/77 (15%)
Query: 199 LTPRSLDLGFTNLGTQSGFVGEMYGGCDLIRSISGPSEADKPMIVELAVAAMEEFLRMAQ 258
LTPRS GF L T G + Y G ++ + G ++ KP+ VE+A+ M++ + +
Sbjct: 93 LTPRS---GFPTLLTSIGAMYAFYRGGIRLKIVPGVADQPKPL-VEVALFTMQDQGYIIK 148
Query: 259 AGDPLWTDQNQWSSVFC 275
A D +S+ FC
Sbjct: 149 AND--------YSTDFC 157
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 30.0 bits (66), Expect = 4.1, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 15/57 (26%)
Query: 73 MEAFFKECPHPDDKQRKELSRELG---------------LEPLQVKFWFQNKRTQMK 114
ME++F E +PD+ +R+E++ + L+V WF N+R ++K
Sbjct: 22 MESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIK 78
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 29.3 bits (64), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 81 PHPDDKQRKELSRELGLEPLQVKFWFQNKRTQM 113
P+P + ++K+++ + L LQV WF N R ++
Sbjct: 33 PYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|1QR4|A Chain A, Two Fibronectin Type-Iii Domain Segment From Chicken
Tenascin
pdb|1QR4|B Chain B, Two Fibronectin Type-Iii Domain Segment From Chicken
Tenascin
Length = 186
Score = 29.3 bits (64), Expect = 7.9, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 430 SPEGRKSMLKLAERMVTSFCTGVGASTAHAWTTLSATGSDDVRVMTRKSMDDPGRPPGIV 489
SP G+K+ +++ + G+ A T + + ++ G + T K G P GI
Sbjct: 43 SPSGKKNEMEIPVDSTSFILRGLDAGTEYTISLVAEKGRHKSKPTTIKGSTVVGSPKGIS 102
Query: 490 LS-----AATSFWIPVPPRRIFDFLR 510
S +AT W PPR D R
Sbjct: 103 FSDITENSATVSW--TPPRSRVDSYR 126
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics Consortium
(Nesg) Target Hr7907f
Length = 74
Score = 29.3 bits (64), Expect = 8.2, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 64 RHTQRQIQEMEAFFKECPHPDDKQRKELSRELGLEPLQVKFWFQNKRTQMKAQHERHENQ 123
+ T+ Q+ E++ + + P D + L + GL ++K WF + R Q NQ
Sbjct: 12 KKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYN---QRNSKSNQ 68
Query: 124 ILKAEN 129
L N
Sbjct: 69 CLHLNN 74
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
0.317 0.132 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,272,668
Number of Sequences: 62578
Number of extensions: 835004
Number of successful extensions: 2032
Number of sequences better than 100.0: 93
Number of HSP's better than 100.0 without gapping: 81
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1950
Number of HSP's gapped (non-prelim): 93
length of query: 673
length of database: 14,973,337
effective HSP length: 105
effective length of query: 568
effective length of database: 8,402,647
effective search space: 4772703496
effective search space used: 4772703496
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)