RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3735
(91 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 = 77.4 bits (191), Expect = 8e-21
Identities = 30/49 (61%), Positives = 39/49 (79%), Gaps = 1/49 (2%)
Query: 11 EDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
ED+S+ E E +L KRKQRR RTTF++ QL+ELE+AF RT YPD++TR
Sbjct: 1 EDISDCESEPGIAL-KRKQRRSRTTFSASQLDELERAFERTQYPDIYTR 48
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 72.8 bits (179), Expect = 5e-19
Identities = 20/35 (57%), Positives = 23/35 (65%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
+R RT+FT Q+E LEK F RTHYPDVF R
Sbjct: 3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFAR 37
>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 = 71.6 bits (176), Expect = 1e-18
Identities = 19/35 (54%), Positives = 20/35 (57%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
RR+RT FT QLE LE F T YPDV TR
Sbjct: 3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTR 37
>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 = 70.5 bits (173), Expect = 5e-18
Identities = 18/35 (51%), Positives = 22/35 (62%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
RR RTTFT QL+ LE F++T YPD+F R
Sbjct: 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMR 37
>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 = 69.3 bits (170), Expect = 1e-17
Identities = 19/32 (59%), Positives = 22/32 (68%)
Query: 28 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
QRR RT FTS QL++LE F R YPD+ TR
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTR 33
>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 = 66.7 bits (163), Expect = 1e-16
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
+R RT+F QL ++ F+ H PD +
Sbjct: 4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLK 38
>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 = 64.3 bits (157), Expect = 1e-15
Identities = 11/34 (32%), Positives = 13/34 (38%)
Query: 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
R RT FT +QL L+ F YP
Sbjct: 4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEF 37
>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 = 63.9 bits (156), Expect = 1e-15
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
RR RT FT Q+E LE F YP +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDIL 31
>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 = 61.6 bits (150), Expect = 9e-15
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 28 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
K R RT QL L ++ PD ++
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKE 34
>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 = 61.5 bits (150), Expect = 1e-14
Identities = 25/27 (92%), Positives = 25/27 (92%)
Query: 33 RTTFTSFQLEELEKAFSRTHYPDVFTR 59
TFTSFQLEELEKAFSRTHYPDVFTR
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTR 29
>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 = 60.0 bits (145), Expect = 8e-14
Identities = 10/36 (27%), Positives = 14/36 (38%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
R R T+ L +E F+ YPD R+
Sbjct: 3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKRE 38
>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 = 59.0 bits (143), Expect = 2e-13
Identities = 12/47 (25%), Positives = 17/47 (36%)
Query: 14 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
S G ++ +R RTT T QLE L + + P
Sbjct: 2 SSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLD 48
>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 = 53.9 bits (130), Expect = 1e-11
Identities = 9/35 (25%), Positives = 13/35 (37%)
Query: 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
+R RT T QL L + F + P +
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIK 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 = 51.6 bits (124), Expect = 9e-11
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTH-YPDVFTR 59
T T Q+E LE F++ + +PD T
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTL 32
>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 = 54.1 bits (129), Expect = 1e-10
Identities = 11/42 (26%), Positives = 17/42 (40%)
Query: 19 EDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
LP +K RR R + + L +A+ R P R+
Sbjct: 105 PTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERE 146
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 52.1 bits (124), Expect = 1e-10
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
P +K RR R + + L +A+ R P R+
Sbjct: 5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERE 40
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 48.6 bits (116), Expect = 1e-09
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTH-YPDVFTR 59
+ + T Q+E LE F++ + +PD T
Sbjct: 3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTL 33
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 51.2 bits (121), Expect = 2e-09
Identities = 9/38 (23%), Positives = 15/38 (39%)
Query: 22 ASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
+ +K RR R + + L +A+ R P R
Sbjct: 135 SEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEER 172
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 46.3 bits (110), Expect = 1e-08
Identities = 8/38 (21%), Positives = 14/38 (36%)
Query: 23 SLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
S Y+ + QL L+ +F R +P +
Sbjct: 2 SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVE 39
>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 = 46.6 bits (110), Expect = 4e-08
Identities = 10/56 (17%), Positives = 20/56 (35%)
Query: 5 SSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
+ + + ++ K+R+ RT+FT +E L F + P
Sbjct: 69 NEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEIT 124
>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 = 43.6 bits (103), Expect = 1e-07
Identities = 6/33 (18%), Positives = 13/33 (39%)
Query: 28 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
+ T Q+ L+ +F ++ +PD
Sbjct: 3 HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVY 35
>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 = 43.8 bits (103), Expect = 4e-07
Identities = 12/56 (21%), Positives = 20/56 (35%)
Query: 5 SSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
S EE G + + ++R+ RTT + + LE+ F P
Sbjct: 63 LSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIM 118
>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 = 42.1 bits (99), Expect = 7e-07
Identities = 16/40 (40%), Positives = 18/40 (45%)
Query: 14 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
S G +K RR RT FT QL LEK F + Y
Sbjct: 2 SSGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKY 41
>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 = 40.5 bits (94), Expect = 8e-06
Identities = 7/51 (13%), Positives = 19/51 (37%)
Query: 9 GEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
++ + + + ++R RT+ + LE F ++ P +
Sbjct: 76 EADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQI 126
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 40.4 bits (94), Expect = 9e-06
Identities = 8/49 (16%), Positives = 15/49 (30%)
Query: 11 EDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
+ S + ++R+ RT+ LE F + P
Sbjct: 81 DSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEI 129
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 37.9 bits (88), Expect = 3e-05
Identities = 12/40 (30%), Positives = 18/40 (45%)
Query: 14 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
+E + K+++ RT F+S QL L F R Y
Sbjct: 7 AENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKY 46
>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 = 39.2 bits (91), Expect = 3e-05
Identities = 9/55 (16%), Positives = 17/55 (30%)
Query: 5 SSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
+ S + ++R+ RT+ + LEK+F P
Sbjct: 77 NLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDI 131
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 37.4 bits (87), Expect = 4e-05
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 27 RKQRRYRTTFTSFQLEELEKAFSRTHY 53
R+ RT ++SFQL L++ F +T Y
Sbjct: 5 SSGRKPRTIYSSFQLAALQRRFQKTQY 31
>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 = 36.8 bits (86), Expect = 4e-05
Identities = 6/35 (17%), Positives = 15/35 (42%)
Query: 26 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
K K + +++ + LE+ F R + ++
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKE 36
>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 = 36.6 bits (85), Expect = 5e-05
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHY 53
RRYRT FT QL LEK F + +Y
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENY 25
>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 = 37.0 bits (86), Expect = 6e-05
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
K+R+ R FT Q ELE+ F + Y
Sbjct: 5 LPNKKRKRRVLFTKAQTYELERRFRQQRY 33
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 37.1 bits (86), Expect = 6e-05
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 21 YASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
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 = 36.6 bits (85), Expect = 6e-05
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
+ + F++ Q ELEK F Y
Sbjct: 3 SGSSGKGGQVRFSNDQTIELEKKFETQKY 31
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 36.1 bits (84), Expect = 1e-04
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 30 RRYRTTFTSFQLEELEKAFSRTHY 53
R+ RT FT+ QL LE+ F + Y
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQY 24
>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 = 36.2 bits (84), Expect = 1e-04
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHY 53
RR RTTFTS Q+ ELE+ F + Y
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRY 26
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 35.8 bits (83), Expect = 1e-04
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 28 KQRRYRTTFTSFQLEELEKAFSRTHY 53
+ + + Q+ ELE+ FS Y
Sbjct: 3 HHHHHHSHMSHTQVIELERKFSHQKY 28
>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 = 35.6 bits (82), Expect = 2e-04
Identities = 11/52 (21%), Positives = 16/52 (30%), Gaps = 3/52 (5%)
Query: 28 KQRRYRTTFTSFQLEELEKAFSRT-HYPDVFTRQCGRFSRQRSMPGELCVAW 78
R RT + L L+ YPD S Q +P + +
Sbjct: 6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIH--TLSAQLDLPKHTIIKF 55
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 34.9 bits (81), Expect = 2e-04
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHY 53
+R+ R F+ Q+ ELE+ F + Y
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRY 26
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 35.0 bits (81), Expect = 3e-04
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 28 KQRRYRTTFTSFQLEELEKAFSRTHY 53
+++ RT F+ QL L+ F + Y
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKY 27
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 34.6 bits (80), Expect = 3e-04
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHY 53
+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 = 35.3 bits (81), Expect = 3e-04
Identities = 12/34 (35%), Positives = 14/34 (41%)
Query: 20 DYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
+ 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 = 34.2 bits (79), Expect = 4e-04
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHY 53
++R RT F+S QL L++ F+ Y
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRY 27
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 33.9 bits (78), Expect = 8e-04
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 28 KQRRYRTTFTSFQLEELEKAFSRTHY 53
+R RT +T QL ELEK F Y
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKY 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 = 34.0 bits (78), Expect = 9e-04
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
+RR R T+T +Q ELEK F HY
Sbjct: 16 TNGLRRRGRQTYTRYQTLELEKEFHTNHY 44
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 33.7 bits (77), Expect = 0.001
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
+ +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 = 32.8 bits (75), Expect = 0.002
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTHY 53
++R R T+T +Q ELEK F Y
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRY 26
>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 = 32.3 bits (73), Expect = 0.004
Identities = 8/45 (17%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 16 GEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
G + P ++++ T Q++ LE +F ++ +P
Sbjct: 1 GSSGSSGAYPDFAPQKFKEK-TQGQVKILEDSFLKSSFPTQAELD 44
>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 = 31.7 bits (71), Expect = 0.009
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAW 78
PK T QL L+ AF RT +P + +++ + V+W
Sbjct: 21 PKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYD--KLAKESGLARTDIVSW 72
>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 = 31.0 bits (70), Expect = 0.013
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 5/38 (13%)
Query: 23 SLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
S P + + R QL LE +F++ P
Sbjct: 6 SGPTKYKER-----APEQLRALESSFAQNPLPLDEELD 38
>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 = 31.0 bits (70), Expect = 0.013
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 21 YASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
L R R+ R +T Q ELEK F Y
Sbjct: 5 ANWLHARSTRKKRCPYTKHQTLELEKEFLFNMY 37
>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 = 30.6 bits (69), Expect = 0.014
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 27 RKQRRYRTTFTSFQLEELEKAFSRTHY 53
R+ R ++ QL ELE+ ++ +
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKF 31
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 30.2 bits (68), Expect = 0.020
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 27 RKQRRYRTTFTSFQLEELEKAFSRTHY 53
+ R+ R +T QL+ELE+ ++ +
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKF 31
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 31.4 bits (70), Expect = 0.020
Identities = 7/44 (15%), Positives = 14/44 (31%)
Query: 17 EMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
+ +++ ++ R FT Q L F P +
Sbjct: 85 KEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQI 128
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 29.6 bits (67), Expect = 0.025
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 34 TTFTSFQLEELEKAFSRTHY 53
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 = 29.2 bits (65), Expect = 0.066
Identities = 6/36 (16%), Positives = 14/36 (38%), Gaps = 5/36 (13%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
P++ + + T+ QL L+ +F +
Sbjct: 12 PQKFKEK-----TAEQLRVLQASFLNSSVLTDEELN 42
>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 = 28.7 bits (63), Expect = 0.26
Identities = 18/90 (20%), Positives = 30/90 (33%), Gaps = 17/90 (18%)
Query: 13 VSEGEMEDYASLPKRKQRRYR--TTFTSFQLEELEKAFS---RTHYP---DVFTRQCGRF 64
+S+ E++ R T S Q E ++K R +Y +
Sbjct: 46 LSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQ--- 102
Query: 65 SRQRSMPGEL---CVAWTHHLNAAFTSSKY 91
RQ SM + ++ N F +KY
Sbjct: 103 -RQPSMMTRMYIEQRDRLYNDNQVF--AKY 129
Score = 25.2 bits (54), Expect = 4.0
Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 22/91 (24%)
Query: 10 EEDVSE--GEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRT--HYPDVFTRQC-GRF 64
+ DV ++ Y SL +++ + + S LE K + H R +
Sbjct: 401 KSDVMVVVNKLHKY-SLVEKQPKESTISIPSIYLELKVKLENEYALH------RSIVDHY 453
Query: 65 SRQRSMPGELCVA------W----THHLNAA 85
+ ++ + + + HHL
Sbjct: 454 NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI 484
>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 = 27.3 bits (60), Expect = 0.35
Identities = 7/46 (15%), Positives = 14/46 (30%), Gaps = 2/46 (4%)
Query: 33 RTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAW 78
T QL L+ F + + + + +P + W
Sbjct: 7 GKRKTKEQLAILKSFFLQCQWAR--REDYQKLEQITGLPRPEIIQW 50
>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 = 27.4 bits (62), Expect = 0.61
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 29 QRRYRTTFTSFQLEELEKAFSRTH 52
QR +R T + E LEK F
Sbjct: 359 QRWHRETESPEMKEWLEKNFIVQR 382
>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 = 26.1 bits (57), Expect = 1.0
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 14 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHY 53
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 = 25.6 bits (55), Expect = 1.7
Identities = 7/34 (20%), Positives = 12/34 (35%)
Query: 27 RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
R R + + L +A+ R P R+
Sbjct: 4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEERE 37
>2r6f_A Excinuclease ABC subunit A; UVRA, nucleotide excision repair, DNA
repair, ABC ATPase, at cassette, DNA damage, DNA
excision; HET: ADP; 3.20A {Geobacillus
stearothermophilus} PDB: 3uwx_A
Length = 972
Score = 25.2 bits (56), Expect = 3.3
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 29 QRRYRTTFTSFQLEELEK 46
+RRYR T + + E++EK
Sbjct: 400 ERRYRETSSDYIREQMEK 417
>2ygr_A Uvrabc system protein A; hydrolase, nucleotide excision repair;
3.40A {Mycobacterium tuberculosis} PDB: 3zqj_A
Length = 993
Score = 25.2 bits (56), Expect = 3.4
Identities = 5/18 (27%), Positives = 7/18 (38%)
Query: 29 QRRYRTTFTSFQLEELEK 46
QR+ T + E E
Sbjct: 409 QRKMSQTESEQMKERYEG 426
>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 = 24.6 bits (53), Expect = 3.4
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 14 SEGEMEDYASLPKRKQRRYRTTFTSFQLEELE 45
S G A ++R+RT FT+ Q E +
Sbjct: 2 SSGSSGSSAEAGGGIRKRHRTKFTAEQKERML 33
>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA
repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A
{Geobacillus}
Length = 670
Score = 25.2 bits (56), Expect = 3.5
Identities = 8/57 (14%), Positives = 18/57 (31%), Gaps = 8/57 (14%)
Query: 6 SGRGEEDVS-EGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQC 61
SG G+ ++ + QRRY + +++ + L +
Sbjct: 53 SGSGKSSLAFDTIY-------AEGQRRYVESLSAYARQFLGQMEKPDVDAIEGLSPA 102
>3kdg_A DNA mismatch repair protein MUTL; endonuclease, DNA damage, DNA
repair, hydrolase; HET: DNA; 2.00A {Bacillus subtilis}
PDB: 3gab_A* 3kdk_A*
Length = 197
Score = 24.0 bits (53), Expect = 8.0
Identities = 6/18 (33%), Positives = 7/18 (38%)
Query: 33 RTTFTSFQLEELEKAFSR 50
R E+EK F R
Sbjct: 178 RPIIIHHSTYEMEKMFKR 195
>2bec_A Calcineurin B homologous protein 2; calcineurin-homologous
protein, calcium-binding protein, NHE1 regulating
protein; 2.70A {Homo sapiens}
Length = 202
Score = 23.9 bits (52), Expect = 9.2
Identities = 9/50 (18%), Positives = 12/50 (24%), Gaps = 13/50 (26%)
Query: 1 MGVPSSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSR 50
MG SS + + T F+ L L F
Sbjct: 1 MGSRSS----HAAVIPDGDSIRR---------ETGFSQASLLRLHHRFRA 37
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 0.130 0.394
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: 1,422,563
Number of extensions: 68193
Number of successful extensions: 195
Number of sequences better than 10.0: 1
Number of HSP's gapped: 193
Number of HSP's successfully gapped: 78
Length of query: 91
Length of database: 6,701,793
Length adjustment: 58
Effective length of query: 33
Effective length of database: 5,082,375
Effective search space: 167718375
Effective search space used: 167718375
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 (21.8 bits)
S2: 51 (23.3 bits)