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= 048771
(814 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 35/53 (66%), Gaps = 4/53 (7%)
Query: 24 EQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 76
+Q+ L Y P+P ++ ++QL+ ++ + P+ I+VWFQN+RC++K+R
Sbjct: 13 KQLHTLRTCYAANPRPDALMKEQLVE----MTGLSPRVIRVWFQNKRCKDKKR 61
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 8 GKTGSLDNGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQ 67
G +GS +T EQ+EALE L+ E P R+QL R+ ++ ++++VWF+
Sbjct: 1 GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKV----HLREEKVEVWFK 56
Query: 68 NRRCREKQRKEAS 80
NRR + ++ +S
Sbjct: 57 NRRAKWRRSGPSS 69
>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 = 18/63 (28%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 80
+T Q+E LE+++ + P R+QL + +++ +++VWFQNRR + ++R+
Sbjct: 16 FTSYQLEELEKVFQKTHYPDVYAREQL----AMRTDLTEARVQVWFQNRRAKWRKRERFG 71
Query: 81 RLQ 83
++Q
Sbjct: 72 QMQ 74
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 24/51 (47%), Positives = 34/51 (66%), Gaps = 4/51 (7%)
Query: 27 EALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 77
+ALER + E KPSS Q+++R L N+E + ++VWF NRR REK+ K
Sbjct: 100 DALERHFGEHSKPSS---QEIMRMAEEL-NLEKEVVRVWFCNRRQREKRVK 146
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 4/73 (5%)
Query: 8 GKTGSLDNGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQ 67
G +GS K + Y+ Q+ LER Y + +R R+ +++ +QI +WFQ
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKR----RKISAATSLSERQITIWFQ 56
Query: 68 NRRCREKQRKEAS 80
NRR +EK+ +S
Sbjct: 57 NRRVKEKKSGPSS 69
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 4/59 (6%)
Query: 17 KYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
K V YT Q++ LER Y + +R R +N+ +Q+ +WFQNRR +EK+
Sbjct: 4 KRVPYTKVQLKELEREYATNKFITKDKR----RRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 4/59 (6%)
Query: 17 KYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
K V YT Q++ LER Y + +R R +N+ +Q+ +WFQNRR +EK+
Sbjct: 10 KRVPYTKVQLKELEREYATNKFITKDKR----RRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 77
+T EQ+ LE+ +H C K S+ + I LS + Q+K+WFQNRR + K+ K
Sbjct: 14 FTSEQLLELEKEFH-CKKYLSLTERSQIAHALKLSEV---QVKIWFQNRRAKWKRIK 66
>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 = 38.5 bits (88), Expect = 0.017, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN+R + K+
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN+R + K+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAKIKK 58
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 37.4 bits (85), Expect = 0.030, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 78
+T +Q++ LE + P R+ E + +N+ +++VWF+NRR + ++R+E
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTRE----EIAVWTNLTEARVRVWFKNRRAKWRKREE 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 = 37.4 bits (85), Expect = 0.033, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 78
+T +Q++ LE + P R+ E + +N+ +++VWF+NRR + ++R+E
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTRE----EIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 37.4 bits (85), Expect = 0.034, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 15 NGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 74
+G +T Q+ LE+ +H S RR ++ + Q+K+WFQNRR ++K
Sbjct: 35 SGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATL----ELNETQVKIWFQNRRMKQK 90
Query: 75 QRK 77
+R+
Sbjct: 91 KRE 93
>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 = 37.4 bits (85), Expect = 0.038, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN R + K+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNERAKIKK 58
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 37.0 bits (84), Expect = 0.039, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 4/52 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCR 72
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN+R +
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAK 53
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 37.0 bits (84), Expect = 0.040, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 16 GKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
G ++ +T Q+E LE+ + P R++L + + +I+VWFQNRR + ++
Sbjct: 1 GSHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRK 56
Query: 76 RKE 78
+++
Sbjct: 57 QEK 59
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 37.0 bits (84), Expect = 0.045, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 76
+T EQ+E LER + P R++L + + + +++VWF NRR R +++
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQR----AKLTEARVQVWFSNRRARWRKQ 60
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 36.6 bits (83), Expect = 0.053, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
++ EQ+ L+R ++E + RRQQL E + QIK+WF+N+R + K+
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFKNKRAKIKK 60
>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 = 36.6 bits (83), Expect = 0.057, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN R + K+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNARAKIKK 58
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 36.2 bits (82), Expect = 0.073, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 77
+T +Q+ LE+ +++ S RR +L + N+ IKVWFQNRR ++K+++
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQL----NLPESTIKVWFQNRRMKDKRQR 60
>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 = 35.8 bits (81), Expect = 0.10, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
++ EQ+ L+R ++E + RRQQL E + QIK+WF N+R + K+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFANKRAKIKK 56
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 35.8 bits (81), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 8 GKTGSLDNGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQ 67
G +GS +T EQ+EALE+ + P R++L + ++ +I+VWF
Sbjct: 1 GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKI----DLPEARIQVWFS 56
Query: 68 NRRCR 72
NRR +
Sbjct: 57 NRRAK 61
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 17 KYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
+ V +T Q LER + + S+ R+ L L + P Q+K+WFQN R + K+
Sbjct: 15 RRVLFTKAQTYELERRFRQQRYLSAPEREHLTS----LIRLTPTQVKIWFQNHRYKTKR 69
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 17 KYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 76
+ V ++ QV LER + + S+ R+ L + ++ P Q+K+WFQN R + K++
Sbjct: 5 RRVLFSQAQVYELERRFKQQKYLSAPEREHLAS----MIHLTPTQVKIWFQNHRYKMKRQ 60
Query: 77 KEASRLQ 83
+ Q
Sbjct: 61 AKDKAAQ 67
>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 = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 17 KYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
+ V +T Q LER + + S+ R+ L L + P Q+K+WFQN R + K+
Sbjct: 12 RRVLFTKAQTYELERRFRQQRYLSAPEREHLAS----LIRLTPTQVKIWFQNHRYKTKR 66
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
YT Q LE+ + + RR ++ R L N+ +Q+K+WFQNRR + K+
Sbjct: 20 YTKHQTLELEKEFLFNMYLTRDRRYEVAR----LLNLTERQVKIWFQNRRMKMKK 70
>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 = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 78
YT Q+ LE+ + S RR +L ++ N+ + IK+WFQNRR + K+ ++
Sbjct: 10 YTRAQLLELEKEFLFNKYISRPRRVEL----AVMLNLTERHIKIWFQNRRMKWKKEED 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 4/59 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEA 79
YT Q LE+ +H + R++ I LS E +QIK+WFQNRR + K+ +A
Sbjct: 27 YTRYQTLELEKEFH---TNHYLTRRRRIEMAHALSLTE-RQIKIWFQNRRMKLKKEIQA 81
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 35.0 bits (79), Expect = 0.18, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCR 72
++ EQ+ +R ++E + RRQQL E + QIK+WFQN+R +
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAK 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 = 34.7 bits (78), Expect = 0.23, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 19 VRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 74
V ++ QV LER + + S+ R QL + S Q+K+WFQNRR + K
Sbjct: 7 VLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTST----QVKIWFQNRRYKSK 58
>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 = 34.7 bits (78), Expect = 0.24, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 25 QVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEASRL 82
QV LER + S+ R L + + Q+K+WFQNRR + K+++ +S L
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTET----QVKIWFQNRRYKTKRKQLSSEL 68
>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 = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCR 72
++ Q++ LER + P R++L + +N+ +I+VWFQNRR R
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQR----TNLTEARIQVWFQNRRAR 72
>pdb|3KQG|A Chain A, Trimeric Structure Of Langerin
pdb|3KQG|B Chain B, Trimeric Structure Of Langerin
pdb|3KQG|C Chain C, Trimeric Structure Of Langerin
pdb|3KQG|D Chain D, Trimeric Structure Of Langerin
pdb|3KQG|E Chain E, Trimeric Structure Of Langerin
pdb|3KQG|F Chain F, Trimeric Structure Of Langerin
Length = 182
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 48/112 (42%), Gaps = 19/112 (16%)
Query: 73 EKQRKEASRLQAVNRKLTAMNKLLMEENDRLQKQVSQLVYENGYFRQHTQSTTLATKD-T 131
EK ++++A+ L M+KLL +ND LQ VSQ YF+ + +L K
Sbjct: 16 EKASALNTKIRALQGSLENMSKLLKRQNDILQ-VVSQGW---KYFKGNFYYFSLIPKTWY 71
Query: 132 SCESVVTSGQHHLTPQHPPRDASPAGLLSIAEETLTEFLSKATGTAVEWVQM 183
S E S HLT S+ E+ EFL K G + W+ +
Sbjct: 72 SAEQFCVSRNSHLT--------------SVTSESEQEFLYKTAGGLIYWIGL 109
>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 = 0.31, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 78
+T Q+E LE+ + P R++L + + +I+VWFQNRR + +++++
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRKQEK 66
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 33.9 bits (76), Expect = 0.33, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 80
+T Q+E LE ++ P + L ++ N+E +I++WFQNRR + K+ S
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKL----NLELDRIQIWFQNRRAKLKRSHRES 63
Query: 81 RL 82
+
Sbjct: 64 QF 65
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 33.9 bits (76), Expect = 0.33, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 77
+T Q+E LE+ + P R++L + + +I+VWFQNRR + ++++
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRKQE 58
>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 = 33.9 bits (76), Expect = 0.35, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 77
YT Q LE+ +H I R++ I LS + +QIK+WFQNRR + K+ +
Sbjct: 10 YTRYQTLELEKEFH---FNRYITRRRRIDIANALS-LSERQIKIWFQNRRMKSKKDR 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 = 33.9 bits (76), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 22 TPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 74
+P+ LE+++ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 373 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 421
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 33.9 bits (76), Expect = 0.36, Method: Composition-based stats.
Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 28 ALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
ALE+ + E KP+S LI E N+E + I+VWF NRR +EK+
Sbjct: 115 ALEKSFMENQKPTS-EDITLIAE---QLNMEKEVIRVWFSNRRQKEKR 158
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 33.9 bits (76), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 8 GKTGSLDNGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQ 67
G +GS + +T Q++ LE L+ + P R+ E + N+ +++VWF+
Sbjct: 1 GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMRE----EVALKINLPESRVQVWFK 56
Query: 68 NRRCR 72
NRR +
Sbjct: 57 NRRAK 61
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 33.9 bits (76), Expect = 0.42, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 28 ALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 114 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFSNRRQKEKR 157
>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 = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRR 70
+TP+ +EAL + + P P+ Q I E N + + ++VWF NRR
Sbjct: 100 FTPQAIEALNAYFEKNPLPTG----QEITEXAKELNYDREVVRVWFSNRR 145
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 33.5 bits (75), Expect = 0.54, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
YT Q LE+ + + RR ++ R + N+ +Q+K+WFQNRR + K+
Sbjct: 8 YTKYQTLELEKEFLFNMYLTRDRRYEVAR----VLNLTERQVKIWFQNRRMKMKK 58
>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 = 33.5 bits (75), Expect = 0.55, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 22 TPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 74
+P+ LE+++ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 13 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.1 bits (74), Expect = 0.57, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 22 TPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 74
+P+ LE+++ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 5 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 53
>pdb|1ITZ|A Chain A, Maize Transketolase In Complex With Tpp
pdb|1ITZ|B Chain B, Maize Transketolase In Complex With Tpp
pdb|1ITZ|C Chain C, Maize Transketolase In Complex With Tpp
Length = 675
Score = 33.1 bits (74), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 45/99 (45%), Gaps = 20/99 (20%)
Query: 202 CSGVAARACGLVGLEPTRVAEILKDRPRGSAILYALTTLAPARDFWLLRYTSVLEDGSL- 260
C+G+A + G V T + D RG+ +R +++ E G +
Sbjct: 430 CNGIALHSPGFVPYCATFF--VFTDYMRGA-----------------MRISALSEAGVIY 470
Query: 261 VVCERSLKNIQNGPTMPPVQHFVRAEMLPSGYLIRPCEG 299
V+ S+ ++GPT P++H V +P+ ++RP +G
Sbjct: 471 VMTHDSIGLGEDGPTHQPIEHLVSFRAMPNILMLRPADG 509
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 33.1 bits (74), Expect = 0.65, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 22 TPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 80
TPEQ+E L + Y P+ + E ++ + ++VWFQN R RE++ +S
Sbjct: 25 TPEQLEILYQKYLLDSNPTRKMLDHIAHEV----GLKKRVVQVWFQNTRARERKSGPSS 79
>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 = 33.1 bits (74), Expect = 0.66, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 78
YT Q LE+ +H + R++ I LS E +QIK+WFQNRR + K+ +
Sbjct: 3 YTRYQTLELEKEFH---FNRYLTRRRRIEIAHALSLTE-RQIKIWFQNRRMKWKKENK 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 = 33.1 bits (74), Expect = 0.70, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 78
YT Q LE+ +H + R++ I LS E +QIK+WFQNRR + K+ +
Sbjct: 9 YTRYQTLELEKEFH---FNRYLTRRRRIEIAHALSLTE-RQIKIWFQNRRMKWKKENK 62
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.7 bits (73), Expect = 0.74, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 22 TPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 74
+P+ LE ++ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 13 SPQARAFLEEVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 61
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 32.7 bits (73), Expect = 0.77, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
YT Q LE+ +H + R++ I LS E +QIK+WFQNRR + K+
Sbjct: 10 YTRYQTLELEKEFH---FNRYLTRRRRIEIAHALSLTE-RQIKIWFQNRRMKWKK 60
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 32.7 bits (73), Expect = 0.82, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 28 ALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 110 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 153
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 32.7 bits (73), Expect = 0.89, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 37 PKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR----KEASRLQAVNRKLTAM 92
P PS +++L ++C I Q+ WF N+R R K+ +E + + A +TA
Sbjct: 27 PYPSEEAKEELAKKC----GITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTAT 82
Query: 93 N 93
N
Sbjct: 83 N 83
>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 = 32.7 bits (73), Expect = 0.91, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 11 GSLDNGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRR 70
GS + ++ EQ+ L+R ++E + RRQQL E + Q+K WF+N R
Sbjct: 1 GSDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQVKGWFKNMR 56
Query: 71 CREKQ 75
+ K+
Sbjct: 57 AKIKK 61
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 32.3 bits (72), Expect = 0.95, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 30 ERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
+R ++E + RRQQL E + QIK+WFQN+R + K+
Sbjct: 2 KREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAKIKK 43
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 32.3 bits (72), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 10/51 (19%)
Query: 28 ALERLYHECPKPSSIRRQQLIRECPILSN---IEPKQIKVWFQNRRCREKQ 75
ALE + +CPKPS+ E L++ +E + ++VWF NRR +EK+
Sbjct: 113 ALESHFLKCPKPSA-------HEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
>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 = 32.3 bits (72), Expect = 0.98, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
YT Q LE+ +H + R++ I LS E +QIK+WFQNRR + K+
Sbjct: 35 YTRYQTLELEKEFH---FNRYLTRRRRIEIAHALSLTE-RQIKIWFQNRRMKWKK 85
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 32.3 bits (72), Expect = 1.0, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 28 ALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 117 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 160
>pdb|2NZZ|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
pdb|2O00|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
Length = 37
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 60 KQIKVWFQNRRCREKQR 76
+QIK+WFQNRR + K+R
Sbjct: 1 RQIKIWFQNRRMKWKKR 17
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 28 ALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 21 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 64
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 28 ALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 118 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 161
>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 = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR---- 76
+T QV LE+ +H+ +S R L R + Q+K WFQNRR + +++
Sbjct: 24 FTRIQVAELEKRFHKQKYLASAERAALARGLKMTDA----QVKTWFQNRRTKWRRQTAEE 79
Query: 77 KEASRLQAVNR 87
+EA R QA NR
Sbjct: 80 REAER-QAANR 89
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The
Antennapedia Homeodomain From Drosophila In Solution By
1h Nuclear Magnetic Resonance Spectroscopy
Length = 68
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRE-CPILSNIEPKQIKVWFQNRRCREKQRKE 78
YT Q LE+ +H + RR ++ C + +QIK+WFQNRR + K+ +
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALC-----LTERQIKIWFQNRRMKWKKENK 62
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 21 YTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
+T Q+ ALER + + S R + ++ Q+K+WFQNRR + K+
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSL----SLTETQVKIWFQNRRAKAKR 57
>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 = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 8 GKTGSLDNGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQ 67
G +GS KY PEQ+ ALE + + P P +L E + ++I WF
Sbjct: 1 GSSGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTR----REIDSWFS 56
Query: 68 NRRCR 72
RR +
Sbjct: 57 ERRKK 61
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 31.2 bits (69), Expect = 2.6, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 46 QLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
Q ++E + N+ KQ+K WFQN+R + K+
Sbjct: 50 QQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>pdb|2PSO|A Chain A, Human Stard13 (Dlc2) Lipid Transfer And Protein
Localization Domain
pdb|2PSO|B Chain B, Human Stard13 (Dlc2) Lipid Transfer And Protein
Localization Domain
pdb|2PSO|C Chain C, Human Stard13 (Dlc2) Lipid Transfer And Protein
Localization Domain
Length = 237
Score = 31.2 bits (69), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 235 YALTTLAP--ARDFWLLR-YTSVLEDGSLVVCERSLKNIQNGPTMPPVQHFVRAEMLPSG 291
Y L ++AP +RDF +LR + + L G + S+++ + + VRA ++ S
Sbjct: 123 YVLNSMAPHPSRDFVVLRTWKTDLPKGMCTLVSLSVEHEE-----AQLLGGVRAVVMDSQ 177
Query: 292 YLIRPCEGGGSIIHIVDHMDLE 313
YLI PC G S + + +DL+
Sbjct: 178 YLIEPCGSGKSRLTHICRIDLK 199
>pdb|2W4E|A Chain A, Structure Of An N-Terminally Truncated Nudix Hydrolase
Dr2204 From Deinococcus Radiodurans
pdb|2W4E|B Chain B, Structure Of An N-Terminally Truncated Nudix Hydrolase
Dr2204 From Deinococcus Radiodurans
Length = 145
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 168 EFLSKATGTAVEWVQMPGMKPGPDSVGIV 196
E L + G A EWV +PG P P G+V
Sbjct: 54 ELLEEVGGAASEWVPLPGFYPQPSISGVV 82
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 8 GKTGSLDNGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQ 67
G +GS R T +Q+ L + + PS ++ I+E S + K IK WF+
Sbjct: 1 GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPS----EEQIKEMADKSGLPQKVIKHWFR 56
Query: 68 NRRCREKQRKEAS 80
N +E+Q +S
Sbjct: 57 NTLFKERQSGPSS 69
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 30.8 bits (68), Expect = 3.6, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 8 GKTGSLDNGKYVRYTPEQVEALERLYHECPKPSSIRRQQLIRECPILSNIEPKQIKVWFQ 67
G +GS Y+ Q+ AL+R + + + R +L + Q+K+WFQ
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASL----GLTQTQVKIWFQ 56
Query: 68 NRRCREKQRKEAS 80
N+R + K+ +S
Sbjct: 57 NKRSKIKKSGPSS 69
>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 = 30.0 bits (66), Expect = 4.7, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 46 QLIRECPILSNIEPKQIKVWFQNRRCREKQ 75
Q ++E + N+ KQ+K WFQN+R + K+
Sbjct: 31 QQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
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
0.319 0.133 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,562,544
Number of Sequences: 62578
Number of extensions: 951290
Number of successful extensions: 2425
Number of sequences better than 100.0: 76
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 55
Number of HSP's that attempted gapping in prelim test: 2383
Number of HSP's gapped (non-prelim): 77
length of query: 814
length of database: 14,973,337
effective HSP length: 107
effective length of query: 707
effective length of database: 8,277,491
effective search space: 5852186137
effective search space used: 5852186137
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)