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= 003071
(850 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: 33 EQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 85
+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 = 45.1 bits (105), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 37/60 (61%), Gaps = 4/60 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 89
+T EQ+EALE L+ E P R+QL R+ ++ ++++VWF+NRR + ++ +S
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKV----HLREEKVEVWFKNRRAKWRRSGPSS 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 = 42.7 bits (99), Expect = 8e-04, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 89
+T Q+E LE+++ + P R+QL + +++ +++VWFQNRR + ++R+
Sbjct: 16 FTSYQLEELEKVFQKTHYPDVYAREQL----AMRTDLTEARVQVWFQNRRAKWRKRERFG 71
Query: 90 RLQ 92
++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 = 42.0 bits (97), Expect = 0.002, Method: Composition-based stats.
Identities = 24/51 (47%), Positives = 34/51 (66%), Gaps = 4/51 (7%)
Query: 36 EALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 86
+ALER + E KPSS Q+++R L N+E + ++VWF NRR REK+ K
Sbjct: 100 DALERHFGEHSKPSS---QEIMRMAEEL-NLEKEVVRVWFCNRRQREKRVK 146
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 20 MIMDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRR 79
M+ K V YT Q++ LER Y + +R R +N+ +Q+ +WFQNRR
Sbjct: 4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKR----RRISATTNLSERQVTIWFQNRR 59
Query: 80 CREKQ 84
+EK+
Sbjct: 60 VKEKK 64
>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: 26 KYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
K V YT Q++ LER Y + +R R +N+ +Q+ +WFQNRR +EK+
Sbjct: 4 KRVPYTKVQLKELEREYATNKFITKDKR----RRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN+R + K+
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAKIKK 60
>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 = 22/57 (38%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 86
+T EQ+ LE+ +H C K S+ + I LS + Q+K+WFQNRR + K+ K
Sbjct: 14 FTSEQLLELEKEFH-CKKYLSLTERSQIAHALKLSEV---QVKIWFQNRRAKWKRIK 66
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
++ 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 = 38.1 bits (87), Expect = 0.023, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 87
+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 = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 87
+T +Q++ LE + P R+ E + +N+ +++VWF+NRR + ++R+E
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTRE----EIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>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 = 37.7 bits (86), Expect = 0.026, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
++ 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 = 37.7 bits (86), Expect = 0.026, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 4/52 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 81
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN+R +
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAK 53
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 37.4 bits (85), Expect = 0.031, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 24 NGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 83
+G +T Q+ LE+ +H S RR ++ + Q+K+WFQNRR ++K
Sbjct: 35 SGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATL----ELNETQVKIWFQNRRMKQK 90
Query: 84 QRK 86
+R+
Sbjct: 91 KRE 93
>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 = 37.4 bits (85), Expect = 0.035, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
++ 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 = 37.4 bits (85), Expect = 0.036, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
++ EQ+ L+R ++E + RRQQL E + QIK+WFQN R + K+
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNARAKIKK 58
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 37.4 bits (85), Expect = 0.037, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 85
+T EQ+E LER + P R++L + + + +++VWF NRR R +++
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQR----AKLTEARVQVWFSNRRARWRKQ 60
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 37.4 bits (85), Expect = 0.038, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 25 GKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
G ++ +T Q+E LE+ + P R++L + + +I+VWFQNRR + ++
Sbjct: 1 GSHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRK 56
Query: 85 RKE 87
+++
Sbjct: 57 QEK 59
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 37.0 bits (84), Expect = 0.043, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 26 KYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR 85
K + Y+ Q+ LER Y + +R R+ +++ +QI +WFQNRR +EK+
Sbjct: 10 KRIPYSKGQLRELEREYAANKFITKDKR----RKISAATSLSERQITIWFQNRRVKEKKS 65
Query: 86 KEAS 89
+S
Sbjct: 66 GPSS 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 = 37.0 bits (84), Expect = 0.051, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR---- 85
+T QV LE+ +H+ +S R L R + Q+K WFQNRR + +++
Sbjct: 24 FTRIQVAELEKRFHKQKYLASAERAALARGLKMTD----AQVKTWFQNRRTKWRRQTAEE 79
Query: 86 KEASRLQAVNR 96
+EA R QA NR
Sbjct: 80 REAER-QAANR 89
>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 = 36.6 bits (83), Expect = 0.066, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
++ EQ+ L+R ++E + RRQQL E + QIK+WF N+R + K+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFANKRAKIKK 56
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 36.2 bits (82), Expect = 0.073, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 22 MDNGKYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 81
M + V ++ QV LER + + S+ R+ L + ++ P Q+K+WFQN R +
Sbjct: 1 MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLAS----MIHLTPTQVKIWFQNHRYK 56
Query: 82 EKQRKEASRLQ 92
K++ + Q
Sbjct: 57 MKRQAKDKAAQ 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 = 36.2 bits (82), Expect = 0.079, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 86
+T +Q+ LE+ +++ S RR +L + N+ IKVWFQNRR ++K+++
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQL----NLPESTIKVWFQNRRMKDKRQR 60
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 35.8 bits (81), Expect = 0.10, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 26 KYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
+ V +T Q LER + + S+ R+ L L + P Q+K+WFQN R + K+
Sbjct: 15 RRVLFTKAQTYELERRFRQQRYLSAPEREHLTS----LIRLTPTQVKIWFQNHRYKTKR 69
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 81
++ EQ+ +R ++E + RRQQL E + QIK+WFQN+R +
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAK 57
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEA 88
YT Q LE+ +H + RR ++ ++ +QIK+WFQNRR + K+ +A
Sbjct: 27 YTRYQTLELEKEFHTNHYLTRRRRIEMAHAL----SLTERQIKIWFQNRRMKLKKEIQA 81
>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 = 0.13, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 26 KYVRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
+ 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: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
YT Q LE+ + + RR ++ R L N+ +Q+K+WFQNRR + K+
Sbjct: 20 YTKHQTLELEKEFLFNMYLTRDRRYEVAR----LLNLTERQVKIWFQNRRMKMKK 70
>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 = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 31/116 (26%), Positives = 52/116 (44%), Gaps = 11/116 (9%)
Query: 237 ILKDRPSWYRDCRSVEVVNVLPTGSSGTIELLYMQLYAPTTLAPARDFWLLR-YTSVLED 295
+L++R W D +VV L + +Y + P+RDF +LR + + L
Sbjct: 94 VLRERHLWDEDFVQWKVVETLDRQTE-----IYQYVLNSMAPHPSRDFVVLRTWKTDLPK 148
Query: 296 GSLVVCERSLNNTQNGPSMPQAPHFVRAEMLPSGYLIRPCEGGGSIIHIVDHMDLE 351
G + S+ + + Q VRA ++ S YLI PC G S + + +DL+
Sbjct: 149 GMCTLVSLSVEHEE-----AQLLGGVRAVVMDSQYLIEPCGSGKSRLTHICRIDLK 199
>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: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 87
YT Q+ LE+ + S RR +L ++ N+ + IK+WFQNRR + K+ ++
Sbjct: 10 YTRAQLLELEKEFLFNKYISRPRRVEL----AVMLNLTERHIKIWFQNRRMKWKKEED 63
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 34.7 bits (78), Expect = 0.20, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 34 QVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEASRL 91
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 = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 81
++ Q++ LER + P R++L + +N+ +I+VWFQNRR R
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQR----TNLTEARIQVWFQNRRAR 72
>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 = 0.25, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 28 VRYTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 83
V ++ QV LER + + S+ R QL + S Q+K+WFQNRR + K
Sbjct: 7 VLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTST----QVKIWFQNRRYKSK 58
>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 = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 31 TPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 83
+P+ LE+++ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 373 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 421
>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 = 34.3 bits (77), Expect = 0.29, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRR 79
+TP+ +EAL + + P P+ + +E N + + ++VWF NRR
Sbjct: 100 FTPQAIEALNAYFEKNPLPTGQEITEXAKEL----NYDREVVRVWFSNRR 145
>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 = 0.30, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 87
+T Q+E LE+ + P R++L + + +I+VWFQNRR + +++++
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRKQEK 66
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 34.3 bits (77), Expect = 0.31, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 86
+T Q+E LE+ + P R++L + + +I+VWFQNRR + ++++
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKI----GLTEARIQVWFQNRRAKWRKQE 58
>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 = 34.3 bits (77), Expect = 0.32, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 37 ALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 114 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFSNRRQKEKR 157
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 33.9 bits (76), Expect = 0.38, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 89
+T Q+E LE ++ P + L ++ N+E +I++WFQNRR + K+ S
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKL----NLELDRIQIWFQNRRAKLKRSHRES 63
Query: 90 RL 91
+
Sbjct: 64 QF 65
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 33.9 bits (76), Expect = 0.38, Method: Composition-based stats.
Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 37 ALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
ALE+ + E KP+S LI E N+E + I+VWF NRR +EK+
Sbjct: 115 ALEKSFMENQKPTS-EDITLIAE---QLNMEKEVIRVWFSNRRQKEKR 158
>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 = 0.42, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRK 86
YT Q LE+ +H + RR + ++ +QIK+WFQNRR + K+ +
Sbjct: 10 YTRYQTLELEKEFHFNRYITRRRRIDIANAL----SLSERQIKIWFQNRRMKSKKDR 62
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 31 TPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKEAS 89
TPEQ+E L + Y P+ + E ++ + ++VWFQN R RE++ +S
Sbjct: 25 TPEQLEILYQKYLLDSNPTRKMLDHIAHEV----GLKKRVVQVWFQNTRARERKSGPSS 79
>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 = 0.49, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 31 TPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 83
+P+ LE+++ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 13 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 61
>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 = 33.5 bits (75), Expect = 0.50, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 87
YT Q LE+ +H + RR ++ ++ +QIK+WFQNRR + K+ +
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL----SLTERQIKIWFQNRRMKWKKENK 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 = 33.5 bits (75), Expect = 0.50, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQRKE 87
YT Q LE+ +H + RR ++ ++ +QIK+WFQNRR + K+ +
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL----SLTERQIKIWFQNRRMKWKKENK 62
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 33.5 bits (75), Expect = 0.56, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
YT Q LE+ + + RR ++ R + N+ +Q+K+WFQNRR + K+
Sbjct: 8 YTKYQTLELEKEFLFNMYLTRDRRYEVAR----VLNLTERQVKIWFQNRRMKMKK 58
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 33.5 bits (75), Expect = 0.57, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
YT Q LE+ +H + RR ++ ++ +QIK+WFQNRR + K+
Sbjct: 10 YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL----SLTERQIKIWFQNRRMKWKK 60
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 33.1 bits (74), Expect = 0.61, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 46 PKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQR----KEASRLQAVNRKLTAM 101
P PS +++L ++C I Q+ WF N+R R K+ +E + + A +TA
Sbjct: 27 PYPSEEAKEELAKKC----GITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTAT 82
Query: 102 N 102
N
Sbjct: 83 N 83
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 33.1 bits (74), Expect = 0.62, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 39 ERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
+R ++E + RRQQL E + QIK+WFQN+R + K+
Sbjct: 2 KREFNENRYLTERRRQQLSSEL----GLNEAQIKIWFQNKRAKIKK 43
>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 = 33.1 bits (74), Expect = 0.66, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 37 ALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 110 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 153
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 33.1 bits (74), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 81
+T EQ+EALE+ + P R++L + ++ +I+VWF NRR +
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERLAAKI----DLPEARIQVWFSNRRAK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 33.1 bits (74), Expect = 0.66, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 31 TPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 83
+P+ LE ++ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 13 SPQARAFLEEVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 61
>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 = 33.1 bits (74), Expect = 0.66, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
++ EQ+ L+R ++E + RRQQL E + Q+K WF+N R + K+
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSEL----GLNEAQVKGWFKNMRAKIKK 61
>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 = 33.1 bits (74), Expect = 0.67, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
YT Q LE+ +H + RR ++ ++ +QIK+WFQNRR + K+
Sbjct: 35 YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL----SLTERQIKIWFQNRRMKWKK 85
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 32.7 bits (73), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 4/48 (8%)
Query: 37 ALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
ALE + +CPKPS+ L +E + ++VWF NRR +EK+
Sbjct: 113 ALESHFLKCPKPSAHEITGLADSL----QLEKEVVRVWFCNRRQKEKR 156
>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 = 32.7 bits (73), Expect = 0.80, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 37 ALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 117 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 160
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 32.7 bits (73), Expect = 0.89, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 37 ALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
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 = 32.7 bits (73), Expect = 0.93, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 37 ALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
ALE+ + E KP+S + + N+E + I+VWF NRR +EK+
Sbjct: 118 ALEKSFLENQKPTSEEITMIADQL----NMEKEVIRVWFCNRRQKEKR 161
>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 = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRE-CPILSNIEPKQIKVWFQNRRCREKQRKE 87
YT Q LE+ +H + RR ++ C + +QIK+WFQNRR + K+ +
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALC-----LTERQIKIWFQNRRMKWKKENK 62
>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: 69 KQIKVWFQNRRCREKQR 85
+QIK+WFQNRR + K+R
Sbjct: 1 RQIKIWFQNRRMKWKKR 17
>pdb|2E42|A Chain A, Crystal Structure Of CEBPBETA BZIP HOMODIMER V285A MUTANT
Bound To A High Affinity Dna Fragment
pdb|2E42|B Chain B, Crystal Structure Of CEBPBETA BZIP HOMODIMER V285A MUTANT
Bound To A High Affinity Dna Fragment
Length = 78
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 75 FQNRRCREKQRKEASRLQAVNRKLTAMNKLL--MEENDRLQKQVSQLVYENTFFR 127
++ RR R SR +A R L +K+L EN+RLQK+V QL E + R
Sbjct: 16 YKIRRERNNIAARKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLR 70
>pdb|1CI6|B Chain B, Transcription Factor Atf4-CEBP BETA BZIP HETERODIMER
Length = 63
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 75 FQNRRCREKQRKEASRLQAVNRKLTAMNKLL--MEENDRLQKQVSQLVYENTFFR 127
++ RR R SR +A R L +K+L EN+RLQK+V QL E + R
Sbjct: 3 YKMRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLR 57
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
+T Q+ ALER + + S R + ++ Q+K+WFQNRR + K+
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSL----SLTETQVKIWFQNRRAKAKR 57
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 30 YTPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCR 81
+T Q++ LE L+ + P R+ E + N+ +++VWF+NRR +
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMRE----EVALKINLPESRVQVWFKNRRAK 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 = 2.8, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 55 QLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
Q ++E + N+ KQ+K WFQN+R + K+
Sbjct: 50 QQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>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 = 30.8 bits (68), Expect = 2.9, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 46 PKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
P PS +++L R+C I Q+ WF N+R R K+
Sbjct: 27 PYPSEEAKEELARKC----GITVSQVSNWFGNKRIRYKK 61
>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 = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 20/45 (44%)
Query: 182 EFLSKATGTAVEWVQMPGMKPGPDSIGIVAISHGCTGVAARACGL 226
E L + G A EWV +PG P P G+V GV A L
Sbjct: 54 ELLEEVGGAASEWVPLPGFYPQPSISGVVFYPLLALGVTLGAAQL 98
>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 = 5.5, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 55 QLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
Q ++E + N+ KQ+K WFQN+R + K+
Sbjct: 31 QQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 29.6 bits (65), Expect = 6.7, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 37 ALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREKQ 84
+LE ++ + PKPS + + + +E ++VWF NRR + K+
Sbjct: 110 SLETMFLKSPKPSLQQITHIANQL----GLEKDVVRVWFSNRRQKGKR 153
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 29.6 bits (65), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 4/53 (7%)
Query: 31 TPEQVEALERLYHECPKPSSMRRQQLIRECPILSNIEPKQIKVWFQNRRCREK 83
+P+ LE+++ +S ++++ ++C I P Q++VWF N+R R K
Sbjct: 5 SPQARAFLEQVFRRKQSLNSKEKEEVAKKC----GITPLQVRVWFINKRMRSK 53
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
0.320 0.134 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,186,460
Number of Sequences: 62578
Number of extensions: 934600
Number of successful extensions: 2032
Number of sequences better than 100.0: 78
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 58
Number of HSP's that attempted gapping in prelim test: 1991
Number of HSP's gapped (non-prelim): 79
length of query: 850
length of database: 14,973,337
effective HSP length: 107
effective length of query: 743
effective length of database: 8,277,491
effective search space: 6150175813
effective search space used: 6150175813
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)