RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5355
(76 letters)
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 65.1 bits (159), Expect = 3e-16
Identities = 21/49 (42%), Positives = 27/49 (55%)
Query: 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
H S Q+ LE+ F KYL+ PERA LA L +TE+QVK+
Sbjct: 2 GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKI 50
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 63.8 bits (156), Expect = 5e-16
Identities = 20/47 (42%), Positives = 32/47 (68%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ R FS Q++ LE+ F+Q +YL+ PER +LA L +T +QVK+
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKI 48
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 64.9 bits (158), Expect = 7e-16
Identities = 24/55 (43%), Positives = 32/55 (58%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ K+K R +F+ Q+ LEK F + KYLA ERA LA L MT++QVK
Sbjct: 9 YQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKT 63
>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 = 64.0 bits (156), Expect = 8e-16
Identities = 20/54 (37%), Positives = 31/54 (57%)
Query: 2 NSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ KK+ R F+ Q + LE+ F Q +YL+ PER LA + +T +QVK+
Sbjct: 2 SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKI 55
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 63.1 bits (154), Expect = 1e-15
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K+ R FS Q+ AL+ F++ KYL+ + +L+ L ++ QVK
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKT 49
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 62.4 bits (152), Expect = 3e-15
Identities = 20/47 (42%), Positives = 31/47 (65%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ R FS Q++ LE+ F+Q KYL+ PER LA + +T +QVK+
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKI 48
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 61.9 bits (151), Expect = 4e-15
Identities = 19/46 (41%), Positives = 31/46 (67%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R F+ Q+ ALE+ F Q +YL+ ERA+ + +L +TE+QVK+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKI 46
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 61.6 bits (150), Expect = 6e-15
Identities = 22/51 (43%), Positives = 37/51 (72%)
Query: 5 KDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ + R +S Q+ AL++ F++T+YLA PERA+LA +LG+T++QVK+
Sbjct: 3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKI 53
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 61.4 bits (149), Expect = 1e-14
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
KK+ TR FS Q+ L F++ KYL+ + +L+ L ++ QVK
Sbjct: 14 KEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKT 68
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 60.4 bits (147), Expect = 1e-14
Identities = 22/41 (53%), Positives = 28/41 (68%)
Query: 15 TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+FS Q+ LE+ F + KYLA ERA LA AL MT++QVK
Sbjct: 3 SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKT 43
>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 = 60.2 bits (146), Expect = 3e-14
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K K + +R F+ Q+ LEK FE+ KYL+ P+R LA +LG+++ QVK
Sbjct: 9 EPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKT 63
>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 = 58.4 bits (142), Expect = 1e-13
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 5 KDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K K + + S Q LE+ F + + L E+ ++A G+T QV+V
Sbjct: 1 KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRV 51
>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 = 58.2 bits (141), Expect = 1e-13
Identities = 22/51 (43%), Positives = 28/51 (54%)
Query: 5 KDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ K + FS Q LEK FE KYL+ PER +LA L ++E QVK
Sbjct: 3 SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKT 53
>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 = 51.7 bits (124), Expect = 6e-11
Identities = 19/46 (41%), Positives = 27/46 (58%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ TR TF+ QI LE+ F Q +YL P A L+ L + +QVK+
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKI 48
>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 = 48.9 bits (117), Expect = 5e-10
Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+K R FS +Q+ L++ F + +YL R +L+ LG+ E+Q+K+
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKI 49
>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 = 48.1 bits (115), Expect = 1e-09
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R F+ Q+ LEK F + Y++ P R +LA L + ES +KV
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKV 47
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 47.8 bits (114), Expect = 1e-09
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K TR ++ Q+ LEK F KY++ P R +LA L +TE +K+
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKI 49
>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 = 48.0 bits (114), Expect = 2e-09
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R F+ +Q+ LEK F KYL+ R ++A L + E+QVK+
Sbjct: 26 VSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKI 80
>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 = 49.2 bits (117), Expect = 3e-09
Identities = 10/55 (18%), Positives = 24/55 (43%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ ++++ R + ALEK+F + + + +A L M + ++V
Sbjct: 93 PGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRV 147
>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 = 47.4 bits (113), Expect = 3e-09
Identities = 10/48 (20%), Positives = 20/48 (41%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ +R F+ Q+ L+ F+ Y E +L+ L + + V
Sbjct: 6 SGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVV 53
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 47.2 bits (112), Expect = 6e-09
Identities = 17/55 (30%), Positives = 31/55 (56%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ + + + K R +++ Q LEK F +YL R ++A+AL +TE Q+K+
Sbjct: 20 STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 74
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 48.5 bits (115), Expect = 7e-09
Identities = 12/55 (21%), Positives = 22/55 (40%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ +K+ R + ALE F + + E LA +L + + V+V
Sbjct: 91 DKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRV 145
>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 = 9e-09
Identities = 10/53 (18%), Positives = 23/53 (43%)
Query: 3 SDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
S + + S +Q+ AL+ +F + ++ E L G++ +V+
Sbjct: 2 SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRK 54
>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 = 46.0 bits (109), Expect = 1e-08
Identities = 17/53 (32%), Positives = 29/53 (54%)
Query: 3 SDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ + ++ R T++ Q LEK F YL R ++A+AL +TE Q+K+
Sbjct: 14 AGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKI 66
>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 = 44.7 bits (106), Expect = 3e-08
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+K R T++ Q LEK F +YL R ++A+AL +TE Q+K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKI 48
>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 = 44.4 bits (105), Expect = 5e-08
Identities = 9/55 (16%), Positives = 23/55 (41%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ + K R T + +Q+ L + + +A+ +G+ + V+V
Sbjct: 9 TGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQV 63
>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 = 45.7 bits (108), Expect = 6e-08
Identities = 13/55 (23%), Positives = 24/55 (43%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ +K+ R T S ALE+ F + + E ++A L + + V+V
Sbjct: 79 EKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRV 133
>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 = 43.2 bits (102), Expect = 9e-08
Identities = 12/49 (24%), Positives = 23/49 (46%)
Query: 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
A H + +QI L+ +F Q+++ E +L G+ S++K
Sbjct: 2 AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKK 50
>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 = 44.2 bits (104), Expect = 2e-07
Identities = 16/48 (33%), Positives = 23/48 (47%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
KK+ R +F+ Q I AL FE+ G E ++A L V+V
Sbjct: 92 KKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRV 139
>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 = 42.9 bits (101), Expect = 2e-07
Identities = 17/54 (31%), Positives = 24/54 (44%)
Query: 2 NSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
N + R ++ Q LEK F YL R ++A L +TE QVK+
Sbjct: 6 NWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKI 59
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 42.0 bits (99), Expect = 3e-07
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 12 TRPTFSGQQIFALEKTFEQT-KYLAGPERAKLAYALGMTESQVKV 55
T + Q+ LE F + K+ +A G+TE Q +
Sbjct: 5 TVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQK 49
>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 = 41.5 bits (98), Expect = 4e-07
Identities = 15/48 (31%), Positives = 28/48 (58%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ R F+ QQ+ LE TF++ +Y R ++A +TE++V+V
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRV 49
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 42.0 bits (99), Expect = 5e-07
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R +F+ +QI ALEK FE+T Y R +LA + + E++++V
Sbjct: 6 SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV 53
>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 = 41.7 bits (98), Expect = 5e-07
Identities = 11/49 (22%), Positives = 26/49 (53%)
Query: 7 AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ + R +S Q+ LE+ + K++ +R K++ A ++E Q+ +
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITI 53
>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 = 41.2 bits (97), Expect = 7e-07
Identities = 16/48 (33%), Positives = 27/48 (56%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R F+ +Q+ ALE F++TKY R +LA + + E +V+V
Sbjct: 6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEV 53
>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 = 41.2 bits (97), Expect = 1e-06
Identities = 19/51 (37%), Positives = 33/51 (64%), Gaps = 6/51 (11%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPE---RAKLAYALGMTESQVKV 55
K++ +R TFS Q+ LE+ FE+T+Y P+ R +LA +TE++++V
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQY---PDIYTREELAQRTNLTEARIQV 64
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 41.0 bits (96), Expect = 1e-06
Identities = 11/54 (20%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 2 NSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ + +KK R ++ Q+ LE+ + K++ +R +++ ++E QV +
Sbjct: 2 SHMLEGRKK--RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTI 53
>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 = 42.6 bits (99), Expect = 1e-06
Identities = 14/74 (18%), Positives = 27/74 (36%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPER 60
+ K + R + L + +E+ K + ER L E + P +
Sbjct: 107 GDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQ 166
Query: 61 AKLAYALGMTESQV 74
A+ + +TE +V
Sbjct: 167 AQGLGSNLVTEVRV 180
>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 = 39.5 bits (93), Expect = 2e-06
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 6/47 (12%)
Query: 12 TRPTFSGQQIFALEKTFEQTKYLAGPE---RAKLAYALGMTESQVKV 55
+ TF+ Q+ LEK F +T Y P+ R +LA +G+TE++++V
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHY---PDVFTREELAMKIGLTEARIQV 45
>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 = 41.3 bits (96), Expect = 3e-06
Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ K+K T + + ++LE F ++ + + +A LG+ + V+V
Sbjct: 90 ETLVQARKRKRT--SIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRV 142
>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 = 39.7 bits (93), Expect = 3e-06
Identities = 10/48 (20%), Positives = 20/48 (41%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K R +F Q+ ++ F + +LA G+T+ ++V
Sbjct: 6 SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQV 53
>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 = 39.7 bits (93), Expect = 3e-06
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ R TF+ Q+ LE F +T+Y R ++A + + ES+V+V
Sbjct: 6 SGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQV 53
>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 = 39.2 bits (92), Expect = 4e-06
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 6/46 (13%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPE---RAKLAYALGMTESQVKV 55
R F+ QI LE F Y P LA L + ++++
Sbjct: 5 RTAFTQNQIEVLENVFRVNCY---PGIDILEDLAQKLNLELDRIQI 47
>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 = 38.9 bits (91), Expect = 5e-06
Identities = 8/50 (16%), Positives = 20/50 (40%)
Query: 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ K R + Q+ L + F+ + + ++A G+ + +K
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKH 53
>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 = 38.9 bits (91), Expect = 6e-06
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 12 TRPTFSGQQIFALEKTFEQT-KYLAGPERAKLAYALGMTESQVKV 55
T + Q+ LE F + K+ +A G+TE Q +
Sbjct: 4 GAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQK 48
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 40.4 bits (93), Expect = 9e-06
Identities = 13/73 (17%), Positives = 27/73 (36%)
Query: 2 NSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERA 61
+ + K + R + L + +++ K + ER L E + P +A
Sbjct: 135 SEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKA 194
Query: 62 KLAYALGMTESQV 74
+ +TE +V
Sbjct: 195 HGLGSNLVTEVRV 207
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 39.9 bits (92), Expect = 1e-05
Identities = 11/48 (22%), Positives = 19/48 (39%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K R F+ Q L F++ K + + ++ LG+ S V
Sbjct: 96 TPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN 143
>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 = 38.5 bits (89), Expect = 2e-05
Identities = 10/67 (14%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAKLAYAL 67
+ +R T+ + + +E F + +Y +R ++A A + + ++
Sbjct: 6 SGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERV---- 61
Query: 68 GMTESQV 74
T +V
Sbjct: 62 --TSLKV 66
>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 = 37.7 bits (88), Expect = 2e-05
Identities = 7/48 (14%), Positives = 17/48 (35%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K R + +Q+ L + + +L G++ ++V
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRV 49
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 36.7 bits (84), Expect = 6e-05
Identities = 14/67 (20%), Positives = 26/67 (38%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAKLAYAL 67
K + R + L + +E+ K + ER L E + P +A+ +
Sbjct: 8 KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSN 67
Query: 68 GMTESQV 74
+TE +V
Sbjct: 68 LVTEVRV 74
>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 = 34.9 bits (80), Expect = 2e-04
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 1 NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
++ K R + +Q+ ALE +F Q E +L MT ++
Sbjct: 2 SSGSSGPTKYKER---APEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDS 53
>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 = 35.0 bits (80), Expect = 3e-04
Identities = 6/47 (12%), Positives = 17/47 (36%)
Query: 9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ Q+ LE +F ++ + E +L ++ ++
Sbjct: 13 APQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDS 59
>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 = 34.2 bits (78), Expect = 6e-04
Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 4/48 (8%)
Query: 8 KKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
K K +Q+ L+ +F + L E +L +T ++
Sbjct: 14 KFKEKTA----EQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDA 57
>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 = 32.9 bits (75), Expect = 0.001
Identities = 6/50 (12%), Positives = 15/50 (30%), Gaps = 1/50 (2%)
Query: 7 AKKKHTRPTFSGQQIFALEKTFEQT-KYLAGPERAKLAYALGMTESQVKV 55
+ +R S + + L+ Y L+ L + + +
Sbjct: 5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIK 54
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding
domain, transcription, structural genomics, NPPSFA; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 72
Score = 29.8 bits (67), Expect = 0.020
Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 19 QQIFALEKTF-EQTKYLAGPERAKLAYALGMTESQVKV 55
+ LEK F TKY L+ L + +++
Sbjct: 18 EPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQC 55
>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 = 30.2 bits (67), Expect = 0.022
Identities = 9/50 (18%), Positives = 21/50 (42%)
Query: 6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
+ + +Q+ L+ F +T++ + E KLA G+ + +
Sbjct: 22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVS 71
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.9 bits (66), Expect = 0.051
Identities = 10/46 (21%), Positives = 17/46 (36%), Gaps = 18/46 (39%)
Query: 25 EKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAKLAYALGMT 70
EK + K KL ++ +K+ + A A A+ T
Sbjct: 18 EK--QALK--------KL-------QASLKLYADDSAP-ALAIKAT 45
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Mus musculus}
SCOP: a.4.1.1
Length = 64
Score = 25.9 bits (57), Expect = 0.49
Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 24 LEKTF-EQTKYLAGPERAKLAYALGMTESQVKV 55
LEK F TK+ L+ L ++
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQR 47
>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 = 26.1 bits (57), Expect = 0.57
Identities = 7/42 (16%), Positives = 18/42 (42%)
Query: 12 TRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQV 53
+ + +Q+ L+ F Q ++ + KL G+ ++
Sbjct: 6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEI 47
>1ffv_B CUTL, molybdoprotein of carbon monoxide dehydrogenase; hydrolase;
HET: ARO PCD FAD; 2.25A {Hydrogenophaga pseudoflava}
SCOP: d.41.1.1 d.133.1.1 PDB: 1ffu_B*
Length = 803
Score = 26.6 bits (59), Expect = 0.67
Identities = 6/21 (28%), Positives = 13/21 (61%)
Query: 39 RAKLAYALGMTESQVKVTGPE 59
R ++ G+ ES+V++ P+
Sbjct: 243 RTVVSMLSGIPESKVRIVSPD 263
>1t3q_B Quinoline 2-oxidoreductase large subunit; QOR, molybdenum, MCD;
HET: FAD MCN; 1.80A {Pseudomonas putida} SCOP: d.41.1.1
d.133.1.1
Length = 788
Score = 26.4 bits (59), Expect = 0.74
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 39 RAKLAYALGMTESQVKVTGPE 59
R +A + E ++V P+
Sbjct: 230 RTMVAMFCAIPEHLIEVRVPD 250
>1n62_B Carbon monoxide dehydrogenase large chain; CODH, molybdenum,
molybdopterin, oxidoreductase; HET: CUB MCN FAD; 1.09A
{Oligotropha carboxidovorans} SCOP: d.41.1.1 d.133.1.1
PDB: 1n5w_B* 1n61_B* 1n60_B* 1n63_B* 1zxi_B*
Length = 809
Score = 26.4 bits (59), Expect = 0.75
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 39 RAKLAYALGMTESQVKVTGPE 59
R ++ G+ E ++ V P+
Sbjct: 246 RTVVSLISGLPEHKIHVIAPD 266
>1rm6_A 4-hydroxybenzoyl-COA reductase alpha subunit; xanthine oxidase
family, dimer heterotrimers, oxidoreductase; HET: PCD
FAD SF4 EPE; 1.60A {Thauera aromatica} SCOP: d.41.1.1
d.133.1.1 PDB: 1sb3_A*
Length = 769
Score = 26.4 bits (59), Expect = 0.98
Identities = 6/21 (28%), Positives = 11/21 (52%)
Query: 39 RAKLAYALGMTESQVKVTGPE 59
K+A L M ++++V P
Sbjct: 220 HLKVAACLQMDSARIRVIKPF 240
>3icj_A Uncharacterized metal-dependent hydrolase; structural genomics,
amidohydrolase, PSI-2, protein structur initiative; HET:
KCX; 1.95A {Pyrococcus furiosus} PDB: 3etk_A* 3igh_X*
Length = 534
Score = 25.7 bits (57), Expect = 1.6
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 36 GPERAKLAYALGMTESQVKVTG 57
G ERAK AY L S K+
Sbjct: 410 GEERAKWAYRLKTLSSITKLGF 431
>2oyo_A Uncharacterized peroxidase-related protein; YP_604910.1,
uncharacterised peroxidase-related, uncharacter
peroxidase-related; 1.51A {Deinococcus geothermalis}
SCOP: a.152.1.3
Length = 196
Score = 24.8 bits (54), Expect = 2.6
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 38 ERAKLAYALGMTESQVKVTGPERAKLAYALGMTESQV 74
E+A AYA +T +VT + L A+G+ + Q+
Sbjct: 128 EQALAAYAEKLTRHPAEVTAADLEPL-RAVGLDDHQI 163
>3r8n_K 30S ribosomal protein S11; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_K 3fih_K* 3iy8_K 2wwl_K
3oar_K 3oaq_K 3ofb_K 3ofa_K 3ofp_K 3ofx_K 3ofy_K 3ofo_K
3r8o_K 4a2i_K 3i1m_K 1vs7_K* 3e1a_C 3e1c_C 1vs5_K
3i1o_K ...
Length = 117
Score = 24.1 bits (53), Expect = 3.8
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 40 AKLAYALGMTESQVKVTGP 58
A G+ +V V GP
Sbjct: 59 ADAVKEYGIKNLEVMVKGP 77
>3c1l_A Putative antioxidant defense protein MLR4105; structural genomics,
joint center for structural genomics, J protein
structure initiative; 2.00A {Mesorhizobium loti}
Length = 188
Score = 24.4 bits (53), Expect = 4.4
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 38 ERAKLAYALGMTESQVKVTGPERAKLAYALGMTESQV 74
+ A L +A+ +TE K+ +RA L G ++ +
Sbjct: 120 QTAMLEFAVKLTEEPAKIVEADRAAL-RKAGFSDRDI 155
>2pfx_A Uncharacterized peroxidase-related protein; YP_614459.1, STR
genomics, joint center for structural genomics, JCSG,
prote structure initiative; HET: MSE PG4; 1.70A
{Silicibacter SP} SCOP: a.152.1.3
Length = 191
Score = 24.4 bits (53), Expect = 4.6
Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 38 ERAKLAYALGMTESQVKVTGPERAKLAYALGMTESQV 74
+R L +A MT + ++ +R L + G + +
Sbjct: 123 QRVMLDFAAKMTRASAEIEEADREVL-RSHGFNDRDI 158
>3hrd_A Nicotinate dehydrogenase large molybdopterin subunit; selenium
ligand, iron, iron-sulfur, metal-binding,
oxidoreductase; HET: MCN FAD; 2.20A {Eubacterium
barkeri}
Length = 425
Score = 24.1 bits (53), Expect = 6.2
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 39 RAKLAYALGMTESQVKVTGPE 59
R ++A L + S+V++
Sbjct: 214 RGEVAGMLALPNSKVRIIQAT 234
>2vqe_K 30S ribosomal protein S11, 30S ribosomal protein S6;
tRNA-binding, rRNA-binding, metal-binding, zinc-finger,
translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}
SCOP: c.55.4.1 PDB: 1gix_N* 1hnw_K* 1hnx_K* 1hnz_K*
1hr0_K 1ibk_K* 1ibl_K* 1ibm_K 1j5e_K 1jgo_N* 1jgp_N*
1jgq_N* 1ml5_N* 1n32_K* 1n33_K* 1n34_K 1n36_K 1xmo_K*
1xmq_K* 1xnq_K* ...
Length = 129
Score = 23.4 bits (51), Expect = 7.2
Identities = 9/19 (47%), Positives = 9/19 (47%)
Query: 40 AKLAYALGMTESQVKVTGP 58
AK A A GM V V G
Sbjct: 69 AKKAMAYGMQSVDVIVRGT 87
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
0.309 0.123 0.330
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,005,430
Number of extensions: 46446
Number of successful extensions: 238
Number of sequences better than 10.0: 1
Number of HSP's gapped: 234
Number of HSP's successfully gapped: 72
Length of query: 76
Length of database: 6,701,793
Length adjustment: 45
Effective length of query: 31
Effective length of database: 5,445,348
Effective search space: 168805788
Effective search space used: 168805788
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (23.3 bits)