RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3734
(158 letters)
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription
regulation; HET: DNA; 2.00A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 3a01_B
Length = 81
Score = 81.6 bits (202), Expect = 2e-21
Identities = 29/48 (60%), Positives = 38/48 (79%), Gaps = 1/48 (2%)
Query: 50 EDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
ED+S+ E E +L KRKQRR RTTF++ QL+ELE+AF RT YPD++T
Sbjct: 1 EDISDCESEPGIAL-KRKQRRSRTTFSASQLDELERAFERTQYPDIYT 47
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 77.4 bits (191), Expect = 8e-20
Identities = 19/34 (55%), Positives = 22/34 (64%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
+R RT+FT Q+E LEK F RTHYPDVF
Sbjct: 3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFA 36
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 76.2 bits (188), Expect = 2e-19
Identities = 18/34 (52%), Positives = 19/34 (55%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
RR+RT FT QLE LE F T YPDV T
Sbjct: 3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGT 36
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the
DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Mus musculus}
Length = 80
Score = 75.1 bits (185), Expect = 7e-19
Identities = 17/34 (50%), Positives = 21/34 (61%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
RR RTTFT QL+ LE F++T YPD+F
Sbjct: 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFM 36
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA
complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P
2lkx_A* 2l7m_P
Length = 68
Score = 72.7 bits (179), Expect = 4e-18
Identities = 18/31 (58%), Positives = 21/31 (67%)
Query: 67 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
QRR RT FTS QL++LE F R YPD+ T
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMST 32
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 70.9 bits (174), Expect = 3e-17
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 65 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
+R RT+F QL ++ F+ H PD
Sbjct: 4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKD 36
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain,
three helices with the DNA binding helix- turn-helix
motif, structural genomics; NMR {Homo sapiens}
Length = 70
Score = 67.4 bits (165), Expect = 5e-16
Identities = 11/33 (33%), Positives = 13/33 (39%)
Query: 65 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
R RT FT +QL L+ F YP
Sbjct: 4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDE 36
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain
variant, DNA binding protein, developmental protein,
disease mutation, DNA-binding; NMR {Homo sapiens}
Length = 67
Score = 66.6 bits (163), Expect = 1e-15
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
RR RT FT Q+E LE F YP +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDI 30
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding
protein, homeodomain, LIM domain; NMR {Rattus
norvegicus} SCOP: a.4.1.1
Length = 66
Score = 64.7 bits (158), Expect = 6e-15
Identities = 9/31 (29%), Positives = 11/31 (35%)
Query: 67 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
K R RT QL L ++ PD
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALM 32
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein,
DNA-binding, N gene regulation; 1.00A {Drosophila
melanogaster} PDB: 3lnq_A 3cmy_A
Length = 60
Score = 63.0 bits (154), Expect = 2e-14
Identities = 24/26 (92%), Positives = 24/26 (92%)
Query: 72 RTTFTSFQLEELEKAFSRTHYPDVFT 97
TFTSFQLEELEKAFSRTHYPDVFT
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFT 28
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription
factor, structural genomics, loop insertion, NPPSFA;
NMR {Homo sapiens} SCOP: a.4.1.1
Length = 95
Score = 63.5 bits (154), Expect = 3e-14
Identities = 9/34 (26%), Positives = 12/34 (35%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
R R T+ L +E F+ YPD
Sbjct: 3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAK 36
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain,
three helices with the DNA binding helix- turn-helix
motif, structural genomics; NMR {Homo sapiens}
Length = 80
Score = 62.1 bits (151), Expect = 8e-14
Identities = 12/45 (26%), Positives = 17/45 (37%)
Query: 53 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
S G ++ +R RTT T QLE L + + P
Sbjct: 2 SSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKM 46
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 58.9 bits (141), Expect = 2e-11
Identities = 11/81 (13%), Positives = 22/81 (27%), Gaps = 1/81 (1%)
Query: 17 SRTGSYSHHSAEDSPSELSDLNRMGVPSSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFT 76
+ S + D P + + + + +K RR R +
Sbjct: 92 RQFNQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDAC-SEPTNKKMRRNRFKWG 150
Query: 77 SFQLEELEKAFSRTHYPDVFT 97
+ L +A+ R P
Sbjct: 151 PASQQILYQAYDRQKNPSKEE 171
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain,
three helices with the DNA binding helix- turn-helix
motif, structural genomics; NMR {Homo sapiens}
Length = 70
Score = 55.0 bits (133), Expect = 3e-11
Identities = 9/33 (27%), Positives = 12/33 (36%)
Query: 65 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
+R RT T QL L + F + P
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQ 36
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 55.6 bits (133), Expect = 4e-11
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
P +K RR R + + L +A+ R P
Sbjct: 5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEE 38
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac
development, riken structural genomics/proteomics
initiative, RSGI, transcription; NMR {Mus musculus}
SCOP: a.4.1.1
Length = 72
Score = 53.2 bits (128), Expect = 1e-10
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTH-YPDVFT 97
T T Q+E LE F++ + +PD T
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTT 31
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation,
DNA-binding, POU domain, diabetes, disease mutation,
MODY3, transcription/DNA comple; 2.60A {Homo sapiens}
SCOP: a.4.1.1 a.35.1.1
Length = 194
Score = 55.7 bits (133), Expect = 2e-10
Identities = 10/40 (25%), Positives = 15/40 (37%)
Query: 58 EDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
LP +K RR R + + L +A+ R P
Sbjct: 105 PTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEE 144
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 50.1 bits (120), Expect = 2e-09
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTH-YPDVFT 97
+ + T Q+E LE F++ + +PD T
Sbjct: 3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTT 32
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 52.0 bits (124), Expect = 3e-09
Identities = 18/108 (16%), Positives = 36/108 (33%), Gaps = 10/108 (9%)
Query: 14 SEYSRTGSYSHHSAEDSPSELSDLNRMGVPSSGRGEEDVS--EGEMEDYASLPKRKQRRY 71
YS++ + +P L + E + + ++ K+R+
Sbjct: 37 PAYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKR 96
Query: 72 RTTFTSFQLEELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNR 119
RT+FT +E L F + P T +A +L+ +
Sbjct: 97 RTSFTPQAIEALNAYFEKNPLPTGQEIT-EMA-------KELNYDREV 136
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 47.8 bits (114), Expect = 2e-08
Identities = 8/36 (22%), Positives = 13/36 (36%)
Query: 62 SLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
S Y+ + QL L+ +F R +P
Sbjct: 2 SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSE 37
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor,
homeodomain, domain swapping, structural oxford protein
production facility, OPPF; 2.70A {Homo sapiens}
Length = 66
Score = 45.9 bits (109), Expect = 9e-08
Identities = 6/31 (19%), Positives = 13/31 (41%)
Query: 67 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFT 97
+ T Q+ L+ +F ++ +PD
Sbjct: 3 HHHHHHRKKTKEQIAHLKASFLQSQFPDDAE 33
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 45.5 bits (108), Expect = 1e-07
Identities = 16/40 (40%), Positives = 18/40 (45%)
Query: 53 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
S G +K RR RT FT QL LEK F + Y
Sbjct: 2 SSGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKY 41
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary,
CPHD, POU domain, transcription factor,
transcription/DNA complex; HET: DNA; 2.30A {Rattus
norvegicus} SCOP: a.4.1.1 a.35.1.1
Length = 146
Score = 45.0 bits (106), Expect = 9e-07
Identities = 12/53 (22%), Positives = 20/53 (37%)
Query: 44 SSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVF 96
S EE G + + ++R+ RTT + + LE+ F P
Sbjct: 63 LSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQ 115
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 41.3 bits (97), Expect = 6e-06
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 7/50 (14%)
Query: 43 PSSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
P+S E + K+++ RT F+S QL L F R Y
Sbjct: 4 PTSAENSVAKKEDK-------VPVKKQKTRTVFSSTQLCVLNDRFQRQKY 46
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 40.1 bits (94), Expect = 1e-05
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 66 RKQRRYRTTFTSFQLEELEKAFSRTHY 92
R+ RT ++SFQL L++ F +T Y
Sbjct: 5 SSGRKPRTIYSSFQLAALQRRFQKTQY 31
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 40.6 bits (95), Expect = 1e-05
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 60 YASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
Y + K+++ RT+FT Q+ ELEK F + Y
Sbjct: 9 YQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKY 41
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 70
Score = 40.1 bits (94), Expect = 2e-05
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
+ + F++ Q ELEK F Y
Sbjct: 3 SGSSGKGGQVRFSNDQTIELEKKFETQKY 31
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription
factor DNA complex, pore, stem cells; HET: DNA; 2.80A
{Mus musculus} PDB: 1ocp_A
Length = 155
Score = 41.6 bits (97), Expect = 2e-05
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 9/76 (11%)
Query: 48 GEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTSTGSIAVFKP 107
++ + + + ++R RT+ + LE F ++ P + T IA
Sbjct: 76 EADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQIT-HIA---- 130
Query: 108 FLLMKLDLVKNRPVQT 123
+L L K+ V+
Sbjct: 131 ---NQLGLEKDV-VRV 142
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic
development, complex (homeodomain/DNA); HET: DNA; NMR
{Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P*
1vnd_A 1qry_A
Length = 77
Score = 39.7 bits (93), Expect = 2e-05
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
K+R+ R FT Q ELE+ F + Y
Sbjct: 5 LPNKKRKRRVLFTKAQTYELERRFRQQRY 33
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA
complex, transcription/DNA complex; 2.00A {Drosophila
melanogaster} SCOP: a.4.1.1
Length = 60
Score = 39.3 bits (92), Expect = 2e-05
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHY 92
RRYRT FT QL LEK F + +Y
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENY 25
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 41.2 bits (96), Expect = 2e-05
Identities = 8/47 (17%), Positives = 15/47 (31%)
Query: 50 EDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVF 96
+ S + ++R+ RT+ LE F + P
Sbjct: 81 DSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAH 127
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding
proteins/DNA), complex, DNA- binding protein, DNA; HET:
DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1
PDB: 1f43_A 1yrn_A*
Length = 61
Score = 39.1 bits (92), Expect = 2e-05
Identities = 6/30 (20%), Positives = 13/30 (43%)
Query: 65 KRKQRRYRTTFTSFQLEELEKAFSRTHYPD 94
K K + +++ + LE+ F R +
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLN 31
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double
helix, helix-turn-helix; NMR {Drosophila melanogaster}
SCOP: a.4.1.1
Length = 68
Score = 38.9 bits (91), Expect = 3e-05
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHY 92
RR RTTFTS Q+ ELE+ F + Y
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRY 26
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU
domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP:
a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A
1oct_C* 1pou_A 1pog_A 1hdp_A
Length = 160
Score = 40.3 bits (94), Expect = 4e-05
Identities = 9/51 (17%), Positives = 17/51 (33%)
Query: 44 SSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPD 94
+ S + ++R+ RT+ + LEK+F P
Sbjct: 77 NLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPT 127
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 38.5 bits (90), Expect = 5e-05
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 67 KQRRYRTTFTSFQLEELEKAFSRTHY 92
+ + + Q+ ELE+ FS Y
Sbjct: 3 HHHHHHSHMSHTQVIELERKFSHQKY 28
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 38.0 bits (89), Expect = 6e-05
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 69 RRYRTTFTSFQLEELEKAFSRTHY 92
R+ RT FT+ QL LE+ F + Y
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQY 24
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 37.6 bits (88), Expect = 1e-04
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 67 KQRRYRTTFTSFQLEELEKAFSRTHY 92
+++ RT F+ QL L+ F + Y
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKY 27
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 37.2 bits (87), Expect = 1e-04
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHY 92
+R+ R F+ Q+ ELE+ F + Y
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRY 26
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 37.3 bits (87), Expect = 1e-04
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHY 92
+R+ R F+ Q+ ELE+ F + Y
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKY 26
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex,
DNA-binding protein, protein/DNA complex; HET: DNA;
2.35A {Homo sapiens} SCOP: a.4.1.1
Length = 97
Score = 37.9 bits (88), Expect = 2e-04
Identities = 12/34 (35%), Positives = 14/34 (41%)
Query: 59 DYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
+ RT FT+ QL ELEK F Y
Sbjct: 25 KVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKY 58
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA
binding protein/DNA), transcription/DNA complex; HET:
DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB:
1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A
1du0_A* 1ztr_A 1enh_A 2p81_A
Length = 61
Score = 36.5 bits (85), Expect = 2e-04
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHY 92
++R RT F+S QL L++ F+ Y
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRY 27
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA
binding, homeodomain, homeotic proteins, development,
specificity; HET: DNA; 2.40A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 9ant_A*
Length = 81
Score = 36.7 bits (85), Expect = 3e-04
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
+RR R T+T +Q ELEK F HY
Sbjct: 16 TNGLRRRGRQTYTRYQTLELEKEFHTNHY 44
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 36.2 bits (84), Expect = 3e-04
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 67 KQRRYRTTFTSFQLEELEKAFSRTHY 92
+R RT +T QL ELEK F Y
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKY 27
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 71
Score = 35.9 bits (83), Expect = 5e-04
Identities = 8/29 (27%), Positives = 10/29 (34%), Gaps = 1/29 (3%)
Query: 67 KQRRYRTTFTSFQLEELEKAFSRT-HYPD 94
R RT + L L+ YPD
Sbjct: 6 SGPRSRTKISLEALGILQSFIHDVGLYPD 34
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 36.4 bits (84), Expect = 5e-04
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
+ +R RT++T +Q ELEK F Y
Sbjct: 24 ANGETKRQRTSYTRYQTLELEKEFHFNRY 52
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA;
NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A
1hom_A 1ftz_A
Length = 68
Score = 35.1 bits (81), Expect = 0.001
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTHY 92
++R R T+T +Q ELEK F Y
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRY 26
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor,
homeodomain, structural genomics, oxford production
facility, OPPF, transcription; 2.60A {Homo sapiens}
Length = 96
Score = 34.8 bits (79), Expect = 0.003
Identities = 11/31 (35%), Positives = 13/31 (41%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPD 94
PK T QL L+ AF RT +P
Sbjct: 21 PKSGSTGKICKKTPEQLHMLKSAFVRTQWPS 51
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 89
Score = 34.2 bits (78), Expect = 0.003
Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 55 GEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPD 94
G + P ++++ T Q++ LE +F ++ +P
Sbjct: 1 GSSGSSGAYPDFAPQKFKEK-TQGQVKILEDSFLKSSFPT 39
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation,
helix-turn-helix, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.4.1.1
Length = 70
Score = 33.3 bits (76), Expect = 0.005
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 66 RKQRRYRTTFTSFQLEELEKAFSRTHY 92
R+ R ++ QL ELE+ ++ +
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKF 31
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA
complex, HOX hexapeptide, TALE homeodomain, homeodomain
interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB:
1san_A
Length = 77
Score = 33.3 bits (76), Expect = 0.006
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 60 YASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
L R R+ R +T Q ELEK F Y
Sbjct: 5 ANWLHARSTRKKRCPYTKHQTLELEKEFLFNMY 37
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 35.4 bits (81), Expect = 0.006
Identities = 47/214 (21%), Positives = 68/214 (31%), Gaps = 75/214 (35%)
Query: 2 DFLKLTNLILILSEYSRTGSYSHHSAED---SPSELSDL--NRMGVPS---SGRGEEDVS 53
F + + + G + + + PS L D N GVPS S ++
Sbjct: 291 SFFVSVRKAITVLFF--IGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN---LT 345
Query: 54 EGEMEDY-----ASLPKRKQ--------RR------YRTTFTSFQLEELEKAF------- 87
+ +++DY + LP KQ + + L L KA
Sbjct: 346 QEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL-TLRKAKAPSGLDQ 404
Query: 88 SRTHYPD---VFTSTGSIAVFKPF---LL------MKLDLVKNR----------PVQTYV 125
SR + + F S + V PF LL + DLVKN PV
Sbjct: 405 SRIPFSERKLKF-SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV---- 459
Query: 126 AYGTGRKKDLVYRRIEVEIKFIPNDLV--IFLTP 157
Y T DL R + I +V I P
Sbjct: 460 -YDTFDGSDL--RVLSGS---ISERIVDCIIRLP 487
Score = 28.5 bits (63), Expect = 1.2
Identities = 31/140 (22%), Positives = 37/140 (26%), Gaps = 58/140 (41%)
Query: 13 LSEYS----RTGSYSHHSAEDSPSELSDLNRM----G------VPSSGRGEEDVSEGEME 58
L EY+ S + L + G VP R E S M
Sbjct: 1764 LGEYAALASLADVMS----------IESLVEVVFYRGMTMQVAVP---RDELGRSNYGM- 1809
Query: 59 DYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTSTG---SIAVFKPFLLMKLDL 115
A P R SF E L+ R V TG I +
Sbjct: 1810 -IAINPGR-------VAASFSQEALQYVVER-----VGKRTGWLVEIVNY---------- 1846
Query: 116 VKNRPVQTYVAYGTGRKKDL 135
N Q YVA G + L
Sbjct: 1847 --NVENQQYVAAGD--LRAL 1862
Score = 25.8 bits (56), Expect = 9.1
Identities = 20/109 (18%), Positives = 33/109 (30%), Gaps = 50/109 (45%)
Query: 40 MGVPSSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSR--THYPDVFT 97
MG M+ Y + + ++R H+ D +
Sbjct: 1631 MG---------------MDLYKTSKAAQ-----------------DVWNRADNHFKDTY- 1657
Query: 98 STG-SIAVFKPFLLMKLDLVKNRPVQTYVAYGTGRKKDLV--YRRIEVE 143
G SI LD+V N PV + +G + K + Y + E
Sbjct: 1658 --GFSI----------LDIVINNPVNLTIHFGGEKGKRIRENYSAMIFE 1694
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 75
Score = 32.6 bits (74), Expect = 0.008
Identities = 9/33 (27%), Positives = 14/33 (42%), Gaps = 5/33 (15%)
Query: 62 SLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPD 94
S P + + R QL LE +F++ P
Sbjct: 6 SGPTKYKER-----APEQLRALESSFAQNPLPL 33
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 32.1 bits (73), Expect = 0.011
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 66 RKQRRYRTTFTSFQLEELEKAFSRTHY 92
+ R+ R +T QL+ELE+ ++ +
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKF 31
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.4 bits (78), Expect = 0.013
Identities = 19/130 (14%), Positives = 40/130 (30%), Gaps = 22/130 (16%)
Query: 24 HHSAED-----SPSELSDLNRMGVPSSGRGEEDVSEGEMEDYASLPKRKQRRYR--TTFT 76
+ +D + + + + V + +S+ E++ R T
Sbjct: 15 QYQYKDILSVFEDAFVDNFDCKDVQDMPKSI--LSKEEIDHIIMSKDAVSGTLRLFWTLL 72
Query: 77 SFQLEELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLDLVKNRPVQTYVAYGTGRKKDLV 136
S Q E ++K + FL+ + + +P Y R D +
Sbjct: 73 SKQEEMVQKFVEEVLRINY-----------KFLMSPIKTEQRQPSMMTRMYIEQR--DRL 119
Query: 137 YRRIEVEIKF 146
Y +V K+
Sbjct: 120 YNDNQVFAKY 129
Score = 33.7 bits (76), Expect = 0.019
Identities = 22/110 (20%), Positives = 41/110 (37%), Gaps = 14/110 (12%)
Query: 52 VSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY-PDVFTSTGSIAVFKPFLL 110
V E +Y L + R S + R + VF +++ +P+L
Sbjct: 83 VEEVLRINYKFLMSPIKTEQRQP--SMMTRMYIEQRDRLYNDNQVFAK-YNVSRLQPYLK 139
Query: 111 MKLDLVKNRPVQTYVAY---GTGRKKDL---VYRRIEVEIKFIPNDLVIF 154
++ L++ RP + + G+G K + V +V+ K IF
Sbjct: 140 LRQALLELRPAKNVLIDGVLGSG-KTWVALDVCLSYKVQCKM-DFK--IF 185
Score = 26.4 bits (57), Expect = 6.4
Identities = 12/111 (10%), Positives = 29/111 (26%), Gaps = 29/111 (26%)
Query: 73 TT----FTSFQLEELEKAFSRTHYPDVFTSTGSIAVFKPFLLMKLD-------------- 114
TT T F S H+ T ++ +L +
Sbjct: 271 TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL 330
Query: 115 -----LVKNRPV--QTYVAYGTGRKKDLVYRRIEV----EIKFIPNDLVIF 154
+++ + + ++ + V E + + + L +F
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF 381
Score = 26.0 bits (56), Expect = 6.6
Identities = 19/120 (15%), Positives = 42/120 (35%), Gaps = 30/120 (25%)
Query: 49 EEDVSE--GEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRT--------HY--PDVF 96
+ DV ++ Y SL +++ + + S LE K + HY P F
Sbjct: 401 KSDVMVVVNKLHKY-SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTF 459
Query: 97 TSTGSIAVFKPFLLMKLDLVKNRPVQTYVAY-----GTGRKKDLVYRRIEVEIKFIPNDL 151
S + LD + +++ + + L +R + ++ +F+ +
Sbjct: 460 DSDD-------LIPPYLD----QYFYSHIGHHLKNIEHPERMTL-FRMVFLDFRFLEQKI 507
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 31.5 bits (72), Expect = 0.015
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 73 TTFTSFQLEELEKAFSRTHY 92
T+F+ Q+ ELE+ F R Y
Sbjct: 2 TSFSRSQVLELERRFLRQKY 21
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain,
transcription factor, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.4.1.1
Length = 89
Score = 30.7 bits (69), Expect = 0.058
Identities = 6/31 (19%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 64 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPD 94
P++ + + T+ QL L+ +F +
Sbjct: 12 PQKFKEK-----TAEQLRVLQASFLNSSVLT 37
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain,
transcription factor, leucine zipper- containing
factor, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: a.4.1.1
Length = 76
Score = 28.4 bits (63), Expect = 0.28
Identities = 7/34 (20%), Positives = 12/34 (35%), Gaps = 5/34 (14%)
Query: 61 ASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPD 94
S +R+ T QL L+ F + +
Sbjct: 1 GSSGSSGKRK-----TKEQLAILKSFFLQCQWAR 29
>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Arabidopsis thaliana} SCOP:
a.4.1.1
Length = 80
Score = 28.4 bits (63), Expect = 0.29
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 53 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 92
S G S +R+RT FT+ Q E++ R +
Sbjct: 2 SSGSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGW 41
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices
with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 102
Score = 28.3 bits (62), Expect = 0.56
Identities = 6/29 (20%), Positives = 10/29 (34%)
Query: 66 RKQRRYRTTFTSFQLEELEKAFSRTHYPD 94
R R + + L +A+ R P
Sbjct: 4 GSSGRNRFKWGPASQQILYQAYDRQKNPS 32
>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger
homeobox family protein, riken structural
genomics/proteomics initiative; NMR {Arabidopsis
thaliana} SCOP: a.4.1.1
Length = 80
Score = 27.3 bits (60), Expect = 0.93
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 53 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFS 88
S G A ++R+RT FT+ Q E + A +
Sbjct: 2 SSGSSGSSAEAGGGIRKRHRTKFTAEQKERML-ALA 36
>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold,
hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4}
PDB: 2o0h_A* 2o0k_A*
Length = 385
Score = 27.4 bits (59), Expect = 2.6
Identities = 17/79 (21%), Positives = 26/79 (32%), Gaps = 9/79 (11%)
Query: 23 SHHSAEDSPSELSDLNRMGVPSSGRGEEDVSEG---------EMEDYASLPKRKQRRYRT 73
S + P + SD R+ D E + Y LP K+ +T
Sbjct: 66 SQWDGKWYPEKFSDYLRLHKIVKIPNNSDKPELFQTYKDKNNKRSRYMGLPNLKRANIKT 125
Query: 74 TFTSFQLEELEKAFSRTHY 92
+T +EE +K Y
Sbjct: 126 QWTREMVEEWKKCRDDIVY 144
>3pih_A Uvrabc system protein A; hydrolase, ABC ATPase, DNA repair,
nucleotide excision repai hydrolase-DNA complex; HET:
DNA; 2.90A {Thermotoga maritima}
Length = 916
Score = 27.0 bits (61), Expect = 3.4
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 68 QRRYRTTFTSFQLEELEKAFSRTH 91
QR +R T + E LEK F
Sbjct: 359 QRWHRETESPEMKEWLEKNFIVQR 382
>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 25.7 bits (55), Expect = 3.7
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 61 ASLPKRKQRRYRTTFTSFQLEELEKAFSR 89
S + RT F+ L L+K +
Sbjct: 1 GSSGSSGALQDRTQFSDRDLATLKKYWDN 29
>1jr2_A Uroporphyrinogen-III synthase; heme biosynthesis, HEAM
biosynthesis, lyase; 1.84A {Homo sapiens} SCOP:
c.113.1.1
Length = 286
Score = 25.9 bits (57), Expect = 6.8
Identities = 10/54 (18%), Positives = 16/54 (29%), Gaps = 3/54 (5%)
Query: 71 YRTTFTSFQLEELEKAFSRTHYPD--VFTS-TGSIAVFKPFLLMKLDLVKNRPV 121
Y+T L +S+ P F S +G K + D +
Sbjct: 189 YQTVAHPGIQGNLNSYYSQQGVPASITFFSPSGLTYSLKHIQELSGDNIDQIKF 242
>2l4h_A Calcium and integrin-binding protein 1; metal binding protei; NMR
{Homo sapiens} PDB: 2l4i_A 2lm5_A
Length = 214
Score = 25.6 bits (56), Expect = 8.5
Identities = 13/67 (19%), Positives = 19/67 (28%), Gaps = 14/67 (20%)
Query: 23 SHHSAEDSPSELSDLNRMGVPSSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEE 82
HH S D MG S +E + +Y L T T ++
Sbjct: 7 HHHHHHSSGHIDDDDKHMGGSGSRLSKEL-----LAEYQDL---------TFLTKQEILL 52
Query: 83 LEKAFSR 89
+ F
Sbjct: 53 AHRRFCE 59
>1twf_A B220, DNA-directed RNA polymerase II largest subunit;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB:
1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A
1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A*
1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 25.8 bits (56), Expect = 9.2
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 115 LVKNRPVQ----TYVAYGTGRKKDLVYRRIEVEIKFIPNDLV 152
LV+N P + YV +G + DL Y + +I+ V
Sbjct: 391 LVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKV 432
>1p3h_A 10 kDa chaperonin; beta barrel, acidic cluster, flexible loop,
structural genomics, PSI, protein structure initiative;
2.80A {Mycobacterium tuberculosis} SCOP: b.35.1.1 PDB:
1hx5_A 1lep_A 1p82_A 1p83_A
Length = 99
Score = 24.4 bits (54), Expect = 9.5
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 114 DLVKNRPVQ-TYVAYGTGRKKDLVYRRIEVEIKFIPNDLVIF 154
D K +P + T VA G GR + +RI +++ D VI+
Sbjct: 31 DTAKEKPQEGTVVAVGPGRWDEDGEKRIPLDVA--EGDTVIY 70
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.135 0.377
Gapped
Lambda K H
0.267 0.0818 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,427,530
Number of extensions: 135781
Number of successful extensions: 286
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 81
Length of query: 158
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 72
Effective length of database: 4,300,587
Effective search space: 309642264
Effective search space used: 309642264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.0 bits)