RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4625
(120 letters)
>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 = 97.4 bits (243), Expect = 2e-28
Identities = 50/59 (84%), Positives = 56/59 (94%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWF+NKRAKIKK+
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 85.1 bits (211), Expect = 2e-23
Identities = 31/67 (46%), Positives = 42/67 (62%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
S ++PRT +S QL+ L+ F + +YL R ELA LGL + Q+KIWFQNKR+KI
Sbjct: 3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62
Query: 72 KKASGQK 78
KK+
Sbjct: 63 KKSGPSS 69
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 81.4 bits (201), Expect = 8e-22
Identities = 27/73 (36%), Positives = 40/73 (54%)
Query: 1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
+ K K+++ RT FS QL L F +YL+ ++ QEL+N L L+ Q+
Sbjct: 7 AENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66
Query: 61 KIWFQNKRAKIKK 73
K WFQN+R K K+
Sbjct: 67 KTWFQNQRMKSKR 79
>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 = 79.0 bits (195), Expect = 4e-21
Identities = 26/64 (40%), Positives = 39/64 (60%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
+R RT F+ Q++ L+ F + RYLT R +L+ +L L AQ+KIWF+N+R + K S
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62
Query: 77 QKNP 80
Q
Sbjct: 63 QHKD 66
>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 = 79.4 bits (196), Expect = 4e-21
Identities = 27/67 (40%), Positives = 40/67 (59%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
K K +R RT F+ QL L+ F + +YL+ R +LA LGL++ Q+K W+QN+R K
Sbjct: 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKW 72
Query: 72 KKASGQK 78
KK+
Sbjct: 73 KKSGPSS 79
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 78.1 bits (193), Expect = 8e-21
Identities = 26/57 (45%), Positives = 39/57 (68%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
++PRT F+ QL L+ +F + +YL+ R E ++ L L E Q+KIWFQN+RAK K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>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 = 77.6 bits (192), Expect = 1e-20
Identities = 16/61 (26%), Positives = 35/61 (57%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
K+ K + +++ S + + L+ F + L + ++E+A + G+ Q+++WF NKR +
Sbjct: 1 KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 60
Query: 72 K 72
K
Sbjct: 61 K 61
>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 = 77.8 bits (192), Expect = 1e-20
Identities = 24/65 (36%), Positives = 37/65 (56%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S K + FS +Q L+ +F +YL+ R+ LA L L+E Q+K WFQN+RAK ++
Sbjct: 5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
Query: 74 ASGQK 78
+
Sbjct: 65 SGPSS 69
>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 = 76.6 bits (189), Expect = 3e-20
Identities = 29/57 (50%), Positives = 41/57 (71%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+R RTAF+ +QL RL+ EF + Y++ RR ELA +L L E+ IK+WFQN+R K K+
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 76.2 bits (188), Expect = 4e-20
Identities = 25/59 (42%), Positives = 39/59 (66%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+++ RT FS QL LK F + +YL+ ++ QEL++ L L+ Q+K WFQN+R K K+
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>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 = 76.9 bits (189), Expect = 6e-20
Identities = 30/65 (46%), Positives = 39/65 (60%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
RT F+ QL+ L+ EF N+YL+ RR E+A L LNE Q+KIWFQN+R K KK
Sbjct: 32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
Query: 74 ASGQK 78
+
Sbjct: 92 REREG 96
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 75.9 bits (187), Expect = 7e-20
Identities = 22/66 (33%), Positives = 32/66 (48%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+ S Q+ L+ +F+ +YL+ R LA L L E Q+KIWFQN+R K K+
Sbjct: 2 GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
Query: 74 ASGQKN 79
Sbjct: 62 KQLSSE 67
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 75.9 bits (187), Expect = 9e-20
Identities = 18/74 (24%), Positives = 33/74 (44%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G S + S EQLS LK F N++ + + L GL+ +++ WF ++R
Sbjct: 1 GSSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
Query: 69 AKIKKASGQKNPLA 82
+ G ++ +
Sbjct: 61 YHCRNLKGSRSGPS 74
>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 = 76.0 bits (187), Expect = 9e-20
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 8 SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67
+ +K+++ R F+ Q L+ F + RYL+ R+ LA+ + L Q+KIWFQN
Sbjct: 1 ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60
Query: 68 RAKIKKASGQKN 79
R K K+A +K
Sbjct: 61 RYKTKRAQNEKG 72
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 75.0 bits (185), Expect = 1e-19
Identities = 25/56 (44%), Positives = 35/56 (62%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
++PR FS Q+ L+ F + RYL+ R +LA+ L L Q+KIWFQN+R K K
Sbjct: 3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 74.9 bits (184), Expect = 4e-19
Identities = 25/73 (34%), Positives = 42/73 (57%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
K K+PRT+F+ Q++ L+ F + +YL R LA L + +AQ+K WFQN+R K
Sbjct: 13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKW 72
Query: 72 KKASGQKNPLALQ 84
++ + ++ Q
Sbjct: 73 RRQTAEEREAERQ 85
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 73.7 bits (181), Expect = 8e-19
Identities = 35/72 (48%), Positives = 44/72 (61%)
Query: 2 RSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIK 61
R S + + KR RT+++ Q L+ EF NRYLT RRR E+A+ L L E QIK
Sbjct: 14 RVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 73
Query: 62 IWFQNKRAKIKK 73
IWFQN+R K KK
Sbjct: 74 IWFQNRRMKWKK 85
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 71.6 bits (176), Expect = 2e-18
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
T+FS Q+ L+ F +YL R LA L + +AQ+K WFQN+R K ++ +
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQT 56
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 71.6 bits (176), Expect = 3e-18
Identities = 31/59 (52%), Positives = 38/59 (64%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
KR RTA++ QL L+ EF N+Y++ RR ELA L L E IKIWFQN+R K KK
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>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 = 72.2 bits (177), Expect = 3e-18
Identities = 30/60 (50%), Positives = 38/60 (63%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+R R ++ Q L+ EF N YLT RRR E+A+ L L E QIKIWFQN+R K+KK
Sbjct: 18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>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 = 71.6 bits (176), Expect = 3e-18
Identities = 22/60 (36%), Positives = 35/60 (58%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S KRPRT + +QL L+ F N +E + +E+A++ GL + IK WF+N K ++
Sbjct: 5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64
>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 = 70.6 bits (173), Expect = 1e-17
Identities = 21/66 (31%), Positives = 40/66 (60%)
Query: 8 SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67
+G ++ ++KR RT + EQL L ++ + T + +A+E+GL + +++WFQN
Sbjct: 9 TGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNT 68
Query: 68 RAKIKK 73
RA+ +K
Sbjct: 69 RARERK 74
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 70.1 bits (172), Expect = 1e-17
Identities = 23/62 (37%), Positives = 37/62 (59%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
++ R FS Q+ L+ F + +YL+ R+ LA+ + L Q+KIWFQN R K+K+ +
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
Query: 77 QK 78
K
Sbjct: 63 DK 64
>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 = 70.1 bits (172), Expect = 1e-17
Identities = 33/65 (50%), Positives = 40/65 (61%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
KR R ++ Q L+ EF NRYLT RRR E+A+ L L E QIKIWFQN+R K KK +
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 76 GQKNP 80
K
Sbjct: 62 KTKGE 66
>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 = 68.2 bits (167), Expect = 8e-17
Identities = 22/60 (36%), Positives = 31/60 (51%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S + RT F+ QL L+ F N Y + ++L+N L L I +WFQN R K +K
Sbjct: 5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>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 = 65.6 bits (160), Expect = 8e-16
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
S R RT S E L L+ + Y + L+ +L L + I +FQN+R +K
Sbjct: 5 SSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVK 64
Query: 73 K 73
Sbjct: 65 H 65
>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 = 67.7 bits (165), Expect = 1e-15
Identities = 18/67 (26%), Positives = 33/67 (49%)
Query: 7 KSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66
G + S+ ++ RT+ L+ F EN+ T +A +L + + I++WF N
Sbjct: 92 SPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSN 151
Query: 67 KRAKIKK 73
+R K K+
Sbjct: 152 RRQKEKR 158
>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 = 65.2 bits (159), Expect = 1e-15
Identities = 23/65 (35%), Positives = 40/65 (61%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S ++ R +S QL L+ E+ N+++T+ +R++++ L+E QI IWFQN+R K KK
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
Query: 74 ASGQK 78
+
Sbjct: 65 SGPSS 69
>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 = 64.5 bits (157), Expect = 2e-15
Identities = 27/65 (41%), Positives = 38/65 (58%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
++ R ++ Q L+ EF N YLT RR E+A L L E Q+KIWFQN+R K+KK
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
Query: 74 ASGQK 78
+ +
Sbjct: 71 INKDR 75
>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 = 64.0 bits (156), Expect = 4e-15
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G KR RT+F QL +K F N + ++LA + GL + +++WFQN R
Sbjct: 1 GSSGS-SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNAR 59
Query: 69 AKIKKASGQKNPLALQLMAQG 89
AK ++ ++ + + G
Sbjct: 60 AKFRRNLLRQENGGVSGPSSG 80
>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 = 65.4 bits (159), Expect = 6e-15
Identities = 15/63 (23%), Positives = 31/63 (49%)
Query: 11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
++++ RT S L+ F E+ + + +A EL L + +++WF N+R +
Sbjct: 82 GANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR 141
Query: 71 IKK 73
K+
Sbjct: 142 EKR 144
>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 = 63.1 bits (154), Expect = 6e-15
Identities = 22/63 (34%), Positives = 32/63 (50%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
K R RT + +QL L+ + N +++L GL+ I++WFQNKR K KK
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 75 SGQ 77
S
Sbjct: 62 SIM 64
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 62.6 bits (152), Expect = 1e-14
Identities = 20/69 (28%), Positives = 40/69 (57%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+ ++ R ++ QL L+ E+ N+++T+ +R+ ++ L+E Q+ IWFQN+R K KK
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
Query: 74 ASGQKNPLA 82
+ +
Sbjct: 65 VINKLKTTS 73
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 64.3 bits (156), Expect = 2e-14
Identities = 14/63 (22%), Positives = 30/63 (47%)
Query: 11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
+ ++++ RT+ L+ F + + LA+ L L + +++WF N+R K
Sbjct: 94 AAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQK 153
Query: 71 IKK 73
K+
Sbjct: 154 EKR 156
>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 = 60.8 bits (148), Expect = 6e-14
Identities = 25/63 (39%), Positives = 39/63 (61%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
+RPRTAF+ Q+ L+ F N Y ++LA +L L +I+IWFQN+RAK+K++
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 77 QKN 79
+
Sbjct: 62 ESQ 64
>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 = 59.8 bits (145), Expect = 1e-13
Identities = 13/64 (20%), Positives = 28/64 (43%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+ + EQ++ LK F ++++ + L GL ++IK WF + R + ++
Sbjct: 2 AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
Query: 74 ASGQ 77
Sbjct: 62 GIVH 65
>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 = 61.6 bits (149), Expect = 2e-13
Identities = 18/63 (28%), Positives = 35/63 (55%)
Query: 11 DKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
+ SK+++ RT+F+ + + L F +N T + E+A EL + +++WF N+R
Sbjct: 88 GEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQT 147
Query: 71 IKK 73
+K
Sbjct: 148 LKN 150
>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 = 58.5 bits (142), Expect = 4e-13
Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G +R RT F+ EQL L+ F E +Y R++LA ++ L E ++++WF+N+R
Sbjct: 1 GSSGS-SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRR 59
Query: 69 AKIKK 73
AK ++
Sbjct: 60 AKWRR 64
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 58.6 bits (142), Expect = 4e-13
Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 17 KRPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
+ + + +Q+ L+ F + N++ +A E GL E Q + WF+ + A+ +++
Sbjct: 3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62
Query: 76 GQKN 79
G +
Sbjct: 63 GLPS 66
>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 = 58.6 bits (142), Expect = 5e-13
Identities = 24/78 (30%), Positives = 43/78 (55%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
S +R RT F+ QL L+ F + RY R+E+A ++ L E+++++WF+N+RAK
Sbjct: 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKC 62
Query: 72 KKASGQKNPLALQLMAQG 89
++ Q+ + G
Sbjct: 63 RQQQQQQQNGGQSGPSSG 80
>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 = 58.5 bits (142), Expect = 6e-13
Identities = 27/66 (40%), Positives = 40/66 (60%)
Query: 8 SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67
G + K++R RT FS QL L+ F +Y R+ELA L EA+I++WFQN+
Sbjct: 10 PGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNR 69
Query: 68 RAKIKK 73
RA+++K
Sbjct: 70 RARLRK 75
>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 = 58.1 bits (141), Expect = 6e-13
Identities = 24/59 (40%), Positives = 39/59 (66%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
++R RT F+ +QL +L+ F NRY R+E+A L EA++++WF+N+RAK +K
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 57.4 bits (139), Expect = 1e-12
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G +R RT+F+ EQ+ L+ EF Y R+ LA ++ L EA+I++WF N+R
Sbjct: 1 GSSGS-SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR 59
Query: 69 AKIKKASGQKNPLALQLMAQG 89
AK ++ +N + G
Sbjct: 60 AKWRREEKLRNQRRQSGPSSG 80
>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 = 58.6 bits (141), Expect = 4e-12
Identities = 18/61 (29%), Positives = 34/61 (55%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
KR RT+ L+ F ++ + ++ +AN+LGL + +++WF N+R K K++
Sbjct: 95 ARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS 154
Query: 75 S 75
S
Sbjct: 155 S 155
>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 = 55.7 bits (135), Expect = 4e-12
Identities = 23/54 (42%), Positives = 34/54 (62%)
Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
F+ QL L+ F+ Y R+ELA ++GL EA+I++WFQN+RAK +K
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 57.2 bits (137), Expect = 1e-11
Identities = 15/66 (22%), Positives = 31/66 (46%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+ K+PR F+ Q L F EN+ ++ + ++ +LGL + + +F N R +
Sbjct: 95 NTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154
Query: 74 ASGQKN 79
+ +
Sbjct: 155 KWLEHH 160
>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 = 53.9 bits (130), Expect = 3e-11
Identities = 14/63 (22%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 18 RPRTAFSGEQLSRLKVEFTE-NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
+ +Q+ L+ F + N++ +A E GL E Q + WF+ + A+ +++ G
Sbjct: 3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62
Query: 77 QKN 79
+
Sbjct: 63 LPS 65
>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 = 51.4 bits (123), Expect = 3e-10
Identities = 15/65 (23%), Positives = 25/65 (38%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S + EQL L+ F +N + L +E + +I WF +R K+
Sbjct: 5 SSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNA 64
Query: 74 ASGQK 78
+K
Sbjct: 65 EETKK 69
>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 = 51.9 bits (124), Expect = 3e-10
Identities = 11/55 (20%), Positives = 21/55 (38%)
Query: 24 SGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78
+ Q+ L+ F ++ + T+ L E L+ +I WF +R
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV 75
>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 = 50.0 bits (119), Expect = 2e-09
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 15/75 (20%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELG---------------LNEA 58
S + R + E L+ ++ F EN+Y E +R+E+AN +
Sbjct: 5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSL 64
Query: 59 QIKIWFQNKRAKIKK 73
++ WF N+R +IK+
Sbjct: 65 KVYNWFANRRKEIKR 79
>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 = 49.6 bits (118), Expect = 2e-09
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 6/63 (9%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
++ KEK EQL L+ F + LT+ L + L +I WF K+
Sbjct: 13 QKFKEKTA------EQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSK 66
Query: 72 KKA 74
Sbjct: 67 ALK 69
>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 = 47.9 bits (113), Expect = 2e-08
Identities = 17/60 (28%), Positives = 23/60 (38%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S + EQL LK F ++ + +LA E GL I WF + R K
Sbjct: 23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82
>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 = 42.5 bits (100), Expect = 7e-07
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 8 SGKDKRSKEKRPRTAFSGEQLSRLKVEF-TENRYLTERRRQELANELGLNEAQIKIWFQN 66
SG K+ E L+ F + +Y E+R + L+ +L + +I+ WF++
Sbjct: 3 SGSSGGIKDSPVNKV---EPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRH 59
Query: 67 KRAKIKKASGQKN 79
+R + K SG +
Sbjct: 60 RRNQDKP-SGPSS 71
>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 = 41.9 bits (98), Expect = 2e-06
Identities = 15/56 (26%), Positives = 24/56 (42%)
Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+ EQL+ LK F + ++ Q+L GL +I WF + R +K
Sbjct: 5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription
regulation, transcriptional repression, DNA- binding
protein; HET: DNA; 2.25A {Saccharomyces cerevisiae}
SCOP: a.4.1.1
Length = 87
Score = 39.5 bits (92), Expect = 2e-05
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 3/75 (4%)
Query: 1 PRSRRIKSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNE 57
+ +S + F+ E + L+ F +N YL + + L L+
Sbjct: 12 LVFNVVTQDMINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSR 71
Query: 58 AQIKIWFQNKRAKIK 72
QIK W N+R K K
Sbjct: 72 IQIKNWVSNRRRKEK 86
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain,
hoogsteen base PAIR, transcription/DNA complex; HET:
5IU; 2.10A {Synthetic} SCOP: a.4.1.1
Length = 60
Score = 37.3 bits (87), Expect = 5e-05
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 23 FSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
F+ E + L+ F +N YL + + L L+ QIK W N+R K K +
Sbjct: 5 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTIT 60
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration
calorimetry, protein-DNA complex, transcription/DNA
complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1
PDB: 1akh_B* 1apl_C* 1yrn_B*
Length = 83
Score = 37.5 bits (87), Expect = 9e-05
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
F+ E + L+ F +N YL + + L L+ QIK W +RAK K
Sbjct: 3 PYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKT 62
Query: 74 AS 75
+
Sbjct: 63 IT 64
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 64
Score = 36.9 bits (86), Expect = 1e-04
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAK 70
S + + L F + Y +E ++ELA + G+ +Q+ WF NKR +
Sbjct: 1 SSGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60
Query: 71 IKK 73
KK
Sbjct: 61 YKK 63
>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 = 38.7 bits (89), Expect = 1e-04
Identities = 12/82 (14%), Positives = 24/82 (29%), Gaps = 21/82 (25%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANEL------------------ 53
K +R R + L + + ++ R+ L E
Sbjct: 111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGL 170
Query: 54 ---GLNEAQIKIWFQNKRAKIK 72
+ E ++ WF N+R +
Sbjct: 171 GSNLVTEVRVYNWFANRRKEEA 192
>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 = 36.9 bits (84), Expect = 1e-04
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEF----TENRYLTERRRQELANELGLNEAQIKIWF 64
G S + RT FS L+ LK + T + + + +A EL ++ ++ W
Sbjct: 1 GSSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWI 60
Query: 65 QNKRAKIKKASGQKNP 80
N+R K + + +
Sbjct: 61 GNRRRKYRLMGIEVSG 76
>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 = 35.9 bits (83), Expect = 2e-04
Identities = 9/40 (22%), Positives = 21/40 (52%)
Query: 36 TENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
++ E+R + L+ +L + I+ WF+ +R + K +
Sbjct: 21 AITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPSG 60
>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein,
protein/DNA complex; HET: DNA; 2.35A {Homo sapiens}
SCOP: a.4.1.1 PDB: 1lfu_P
Length = 87
Score = 36.3 bits (84), Expect = 2e-04
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+R R F+ + L F + Y +E ++ELA + G+ +Q+ WF NKR + KK
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
Query: 74 ASGQ 77
G+
Sbjct: 62 NIGK 65
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian,
protein-DNA complex, HOX hexapeptide, TALE homeodomain,
homeodomain interaction; 1.90A {Homo sapiens} SCOP:
a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*
Length = 73
Score = 35.8 bits (83), Expect = 3e-04
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+R R F+ + L F + Y +E ++ELA + G+ +Q+ WF NKR + KK
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
Query: 74 ASGQ 77
G+
Sbjct: 62 NIGK 65
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 37.7 bits (86), Expect = 3e-04
Identities = 12/82 (14%), Positives = 24/82 (29%), Gaps = 21/82 (25%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANEL------------------ 53
K +R R + L + + ++ R+ L E
Sbjct: 138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGL 197
Query: 54 ---GLNEAQIKIWFQNKRAKIK 72
+ E ++ WF N+R +
Sbjct: 198 GSNLVTEVRVYNWFANRRKEEA 219
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 35.5 bits (82), Expect = 5e-04
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAK 70
E + L+ E+R Y +E+ + L+ + L+ Q+ WF N R +
Sbjct: 3 HHHHHHSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRR 62
Query: 71 IKKASGQK 78
+ +K
Sbjct: 63 LLPDMLRK 70
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain,
structural genomics, NPPSFA, national project on
protein structural and functional analyses; NMR {Homo
sapiens}
Length = 70
Score = 35.2 bits (80), Expect = 6e-04
Identities = 10/50 (20%), Positives = 23/50 (46%)
Query: 27 QLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
+ L+ + ++ L E +L+ L+ Q+ WF ++ + + SG
Sbjct: 17 DIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAEVSG 66
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 34.6 bits (79), Expect = 7e-04
Identities = 11/48 (22%), Positives = 20/48 (41%)
Query: 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
LS LK + N + ++A+ + L +K WF+ +A
Sbjct: 13 NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 34.2 bits (79), Expect = 9e-04
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 20 RTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
F + ++ ++ Y +E ++++LA + GL Q+ WF N R +I +
Sbjct: 2 SGIFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMI 61
Query: 77 QKNPLA 82
++ A
Sbjct: 62 DQSNRA 67
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 73
Score = 34.3 bits (79), Expect = 0.001
Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 13 RSKEKRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRA 69
S K R + ++ ++ Y TE ++++A + L Q+ WF N R
Sbjct: 4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARR 63
Query: 70 KIKKAS 75
+I ++
Sbjct: 64 RILQSG 69
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein,
X-linked TGF(beta) induced transcription factor 2-like
protein, TGIF-like on the X; NMR {Homo sapiens}
Length = 83
Score = 33.6 bits (77), Expect = 0.002
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 13 RSKEKRPRTAFSGEQLSRLKVEFTENR---YLTERRRQELANELGLNEAQIKIWFQNKRA 69
S K+ + E + L+ ++R Y +E +Q L+ + L+ QI WF N R
Sbjct: 4 GSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARR 63
Query: 70 KIKK 73
+I
Sbjct: 64 RILP 67
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 34.0 bits (77), Expect = 0.003
Identities = 12/80 (15%), Positives = 24/80 (30%), Gaps = 21/80 (26%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANEL--------------------- 53
K +R R + L + + ++ R+ L E
Sbjct: 8 KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSN 67
Query: 54 GLNEAQIKIWFQNKRAKIKK 73
+ E ++ WF N+R +
Sbjct: 68 LVTEVRVYNWFANRRKEEAF 87
>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 = 32.3 bits (73), Expect = 0.007
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 4/66 (6%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRR----QELANELGLNEAQIKIWFQNKRA 69
KR RT F+ EQ ++ + ++ ++ E G+ +KIW N +
Sbjct: 15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKN 74
Query: 70 KIKKAS 75
+
Sbjct: 75 SGPSSG 80
>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 = 31.9 bits (72), Expect = 0.010
Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 6/66 (9%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRR-----QELANELGLNEAQIKIWFQNKR 68
KR RT F+ EQ R+ E +R+ Q E G+ +K+W N +
Sbjct: 15 GIRKRHRTKFTAEQKERML-ALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNK 73
Query: 69 AKIKKA 74
+
Sbjct: 74 HSGPSS 79
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding
cooperativity, maltose binding protein, MBP, sugar
binding, DNA binding protein; 2.10A {Escherichia coli}
SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A
Length = 421
Score = 33.2 bits (76), Expect = 0.012
Identities = 15/57 (26%), Positives = 30/57 (52%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
+ A S + + L+ F + L + ++E+A + G+ Q+++WF NKR + K
Sbjct: 365 QTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices
with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 31.7 bits (71), Expect = 0.013
Identities = 9/45 (20%), Positives = 21/45 (46%)
Query: 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
+ +S LK + N +++ +GL + +K WF+ ++
Sbjct: 15 DHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY 59
>2gez_A L-asparaginase alpha subunit; isoaspartyl aminopeptidase,
NTN-hydrolase, autoproteolysis, taspase, sodium binding,
hydrolase; 2.60A {Lupinus luteus}
Length = 195
Score = 29.7 bits (67), Expect = 0.16
Identities = 13/86 (15%), Positives = 30/86 (34%), Gaps = 13/86 (15%)
Query: 16 EKRPRTAFSG---EQLSRLK-VEFTENRYL-TERRRQELANELGLNEAQIKIWFQNKRAK 70
+K P + + ++ + VE ++ +L T + L + N Q+ N
Sbjct: 117 DKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEANRVQVDYSQYNYPEP 176
Query: 71 IKKASGQKNPLALQLMAQGLYNHSTV 96
+K + ++ P S +
Sbjct: 177 VKDDAEKELP--------LTNGDSQI 194
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 28.4 bits (63), Expect = 0.54
Identities = 12/57 (21%), Positives = 27/57 (47%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
S +K+P T E RLK + + + ++ +A+++G+ ++ + F A
Sbjct: 1 STKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINAL 57
>3ttq_A Dextransucrase; (beta/alpha)8 barrel, transferase; HET: PG4; 1.90A
{Leuconostoc mesenteroides} PDB: 3tto_A*
Length = 1108
Score = 28.5 bits (63), Expect = 0.59
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 57 EAQIKIWFQNKRAKIKKASGQKNPLALQLMAQGLYNHSTVP 97
+A ++++++++RA KK + P LM L N TVP
Sbjct: 593 KAGLELFYKDQRATNKKYNSYNIPSIYALM---LTNKDTVP 630
>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 = 27.5 bits (60), Expect = 1.4
Identities = 12/96 (12%), Positives = 33/96 (34%), Gaps = 20/96 (20%)
Query: 36 TENR----YLTERRRQELA---NELGLNEAQIK----IWFQNKRAKIKKASGQKNPLALQ 84
T + +L+ ++ + + L ++K + + + + NP L
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331
Query: 85 LMAQGL---------YNHSTVPMSDEEMEMELSLLN 111
++A+ + + H +E L++L
Sbjct: 332 IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE 367
>2in3_A Hypothetical protein; DSBA family, FRNE-like subfamily, disulfide
isomerase, struc genomics, PSI-2, protein structure
initiative; 1.85A {Nitrosomonas europaea}
Length = 216
Score = 26.1 bits (57), Expect = 3.0
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 35 FTENRYLTERRRQ-ELANELGLNEAQIKIWFQNKRAK 70
+ + + +LA +LG+ E++ FQ+ AK
Sbjct: 123 YVGQEDVAQLAILKKLAVDLGIPESRFTPVFQSDEAK 159
>1s8n_A Putative antiterminator; RV1626, structural genomics,
transcriptional antiterminator, component system, PSI;
1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB:
1sd5_A
Length = 205
Score = 25.4 bits (56), Expect = 4.3
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 11/65 (16%)
Query: 20 RTAFSG-EQLSRLKVEFT------ENRYLTERRRQELANELGLNEAQIKIWFQ----NKR 68
A S +++ L+ E E R L ER + L + G+ E W Q ++R
Sbjct: 126 ELAVSRFREITALEGEVATLSERLETRKLVERAKGLLQTKHGMTEPDAFKWIQRAAMDRR 185
Query: 69 AKIKK 73
+K+
Sbjct: 186 TTMKR 190
>3gyk_A 27KDA outer membrane protein; APC61738.2, silicibacter pomeroyi
DSS-3, thioredoxin-like, oxidoreductase, structural
genomics, PSI-2; HET: MSE; 1.76A {Silicibacter pomeroyi}
Length = 175
Score = 25.4 bits (56), Expect = 4.6
Identities = 6/36 (16%), Positives = 13/36 (36%)
Query: 35 FTENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
+ E +A E+GL+ Q++ +
Sbjct: 92 MGMSGKANETGVLRIAREVGLDTEQLQRDMEAPEVT 127
>3qwu_A DNA ligase; structural genomics, PSI-2, midwest center for
structural GE MCSG; HET: DNA ADN; 2.35A {Aquifex
aeolicus}
Length = 370
Score = 25.2 bits (55), Expect = 5.8
Identities = 10/40 (25%), Positives = 17/40 (42%)
Query: 34 EFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+ E +L++ + EL + L +I F IKK
Sbjct: 161 KKNEQGFLSQEEKMELIEKYNLPHVEILGRFTASEEGIKK 200
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational
analysis, G protein, GAS subunit, A2A adenosine
receptor, cell-penetrating peptides; NMR {Synthetic}
PDB: 2o00_A
Length = 37
Score = 23.5 bits (50), Expect = 6.7
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 59 QIKIWFQNKRAKIKK 73
QIKIWFQN+R K KK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>3gx0_A GST-like protein YFCG; transferase, glutathione, glutathione
disulfide, disulfide bond oxidoreductase; HET: GDS;
2.30A {Escherichia coli}
Length = 215
Score = 24.9 bits (55), Expect = 7.1
Identities = 4/16 (25%), Positives = 7/16 (43%)
Query: 32 KVEFTENRYLTERRRQ 47
+ + RY E +R
Sbjct: 125 TIPYAIERYQVETQRL 140
>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix,
transcription/DNA complex; HET: DNA; 1.80A
{Enterobacteria phage lambda} SCOP: a.35.1.2 PDB:
1lrp_A 1rio_A 1lli_A*
Length = 92
Score = 24.2 bits (52), Expect = 7.1
Identities = 12/56 (21%), Positives = 27/56 (48%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRA 69
S +K+P T E RLK + + + ++ +A+++G+ ++ + F A
Sbjct: 1 STKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINA 56
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
0.310 0.125 0.334
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,596,905
Number of extensions: 83195
Number of successful extensions: 307
Number of sequences better than 10.0: 1
Number of HSP's gapped: 290
Number of HSP's successfully gapped: 101
Length of query: 120
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,412,271
Effective search space: 167666298
Effective search space used: 167666298
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 (21.8 bits)
S2: 51 (23.4 bits)