RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1653
(96 letters)
>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 = 120 bits (303), Expect = 1e-37
Identities = 65/68 (95%), Positives = 65/68 (95%)
Query: 1 MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
G NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHAL LTERQIKIWFQNRRM
Sbjct: 14 AGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRM 73
Query: 61 KLKKEIQA 68
KLKKEIQA
Sbjct: 74 KLKKEIQA 81
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 118 bits (296), Expect = 1e-36
Identities = 52/64 (81%), Positives = 55/64 (85%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
ANG +R R +YTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK
Sbjct: 23 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82
Query: 62 LKKE 65
KKE
Sbjct: 83 WKKE 86
>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 = 117 bits (295), Expect = 2e-36
Identities = 35/67 (52%), Positives = 41/67 (61%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
G R +T Q ELEKEFH N YL+R RR+E+A L L E Q+KIWFQNRRMK
Sbjct: 29 PGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMK 88
Query: 62 LKKEIQA 68
KK +
Sbjct: 89 QKKRERE 95
>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 = 111 bits (280), Expect = 2e-34
Identities = 54/66 (81%), Positives = 58/66 (87%)
Query: 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
+R+RGRQTYTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNRRMK KKE
Sbjct: 1 MRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60
Query: 66 IQAIKE 71
+ E
Sbjct: 61 NKTKGE 66
>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 = 108 bits (270), Expect = 9e-33
Identities = 40/59 (67%), Positives = 46/59 (77%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
R+ R YT++QTLELEKEF N YLTR RR E+A L LTERQ+KIWFQNRRMK+KK
Sbjct: 13 TRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKI 71
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 107 bits (268), Expect = 1e-32
Identities = 40/61 (65%), Positives = 45/61 (73%)
Query: 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
G +R R YTR Q LELEKEF N Y++R RR+E+A L LTER IKIWFQNRRMK KK
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 65 E 65
E
Sbjct: 61 E 61
>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 = 105 bits (263), Expect = 9e-32
Identities = 26/67 (38%), Positives = 37/67 (55%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
RR R T+T Q ELE+ F YLT R +++ L L Q+KIWF+NRR + K +
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61
Query: 67 QAIKELN 73
K+ +
Sbjct: 62 DQHKDQS 68
>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 = 105 bits (263), Expect = 9e-32
Identities = 26/62 (41%), Positives = 39/62 (62%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
+ G+ ++ QT+ELEK+F T YL+ R +A L L+ERQ+K WFQNRR K ++
Sbjct: 7 GKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG 66
Query: 67 QA 68
+
Sbjct: 67 PS 68
>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 = 103 bits (258), Expect = 5e-31
Identities = 27/59 (45%), Positives = 41/59 (69%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
R+ R Y++ Q ELE+E+ N ++T+ +R +++ A L+ERQI IWFQNRR+K KK
Sbjct: 7 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 102 bits (255), Expect = 2e-30
Identities = 29/67 (43%), Positives = 44/67 (65%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
R+ R YT+ Q ELE+E+ TN ++T+ +R ++ L+ERQ+ IWFQNRR+K KK I
Sbjct: 7 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 66
Query: 67 QAIKELN 73
+K +
Sbjct: 67 NKLKTTS 73
>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 = 101 bits (253), Expect = 2e-30
Identities = 31/58 (53%), Positives = 40/58 (68%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
RR R +TR Q LEKEF+ +Y++R RR E+A L L E IK+WFQNRRMK K++
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>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 = 101 bits (254), Expect = 2e-30
Identities = 27/67 (40%), Positives = 38/67 (56%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
RR R +T Q + LEK F YL+ RI++A +L L++ Q+K W+QNRRMK
Sbjct: 12 TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71
Query: 62 LKKEIQA 68
KK +
Sbjct: 72 WKKSGPS 78
>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 = 100 bits (252), Expect = 4e-30
Identities = 27/57 (47%), Positives = 39/57 (68%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
+R R ++ Q L++EF+ N YLT RRR +++ L L E QIKIWF+N+R K+KK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 96.9 bits (241), Expect = 3e-28
Identities = 28/72 (38%), Positives = 40/72 (55%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
R++ R ++TR Q ELEK FH YL R +A L +T+ Q+K WFQNRR K +++
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT 76
Query: 67 QAIKELNEQEKQ 78
+E Q
Sbjct: 77 AEEREAERQAAN 88
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 89.4 bits (222), Expect = 2e-25
Identities = 25/62 (40%), Positives = 37/62 (59%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
R+ R Y+ +Q L++ F YL R E+A +L LT+ Q+KIWFQN+R K+KK
Sbjct: 7 GRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSG 66
Query: 67 QA 68
+
Sbjct: 67 PS 68
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 84.3 bits (209), Expect = 1e-23
Identities = 25/64 (39%), Positives = 35/64 (54%)
Query: 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
G + Q +ELE++F YL+ R +A L LTE Q+KIWFQNRR K K+
Sbjct: 2 GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
Query: 65 EIQA 68
+ +
Sbjct: 62 KQLS 65
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 84.5 bits (209), Expect = 2e-23
Identities = 19/61 (31%), Positives = 36/61 (59%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
+++ R ++ Q L F YL+ ++ E+++ L L+ +Q+K WFQN+RMK K+
Sbjct: 22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ 81
Query: 67 Q 67
+
Sbjct: 82 K 82
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 83.1 bits (206), Expect = 3e-23
Identities = 27/57 (47%), Positives = 36/57 (63%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
R+ R +T Q L LE++F YL+ R E + +L LTE Q+KIWFQNRR K 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 = 83.0 bits (206), Expect = 3e-23
Identities = 15/56 (26%), Positives = 29/56 (51%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
+G+ + + LE+ F L + + E+A +T Q+++WF N+RM+ K
Sbjct: 6 PKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 81.6 bits (202), Expect = 2e-22
Identities = 20/61 (32%), Positives = 37/61 (60%)
Query: 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
G +++ R +++ Q L+ F YL+ ++ E++ L L+ +Q+K WFQN+RMK K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Query: 65 E 65
Sbjct: 61 W 61
>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 = 81.3 bits (201), Expect = 3e-22
Identities = 26/67 (38%), Positives = 36/67 (53%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
G +R+ R +T+ QT ELE+ F YL+ R +A + LT Q+KIWFQN R K
Sbjct: 4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63
Query: 62 LKKEIQA 68
K+
Sbjct: 64 TKRAQNE 70
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 78.1 bits (193), Expect = 3e-21
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 13 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
+++R Q LELE+ F YL R +A AL +T+ Q+K WFQNRR K +++
Sbjct: 3 SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 78.0 bits (193), Expect = 3e-21
Identities = 26/57 (45%), Positives = 35/57 (61%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
RR+ R +++ Q ELE+ F YL+ R ++A L LT Q+KIWFQNRR K K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 79.2 bits (195), Expect = 1e-20
Identities = 19/58 (32%), Positives = 28/58 (48%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
RR+ R + + LEK F N T +A L + + I++WF NRR K K+
Sbjct: 101 RRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 74.7 bits (184), Expect = 9e-20
Identities = 24/66 (36%), Positives = 38/66 (57%)
Query: 6 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
+RR+ R +++ Q ELE+ F YL+ R +A + LT Q+KIWFQN R K+K++
Sbjct: 1 MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
Query: 66 IQAIKE 71
+
Sbjct: 61 AKDKAA 66
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 68.9 bits (168), Expect = 2e-16
Identities = 18/68 (26%), Positives = 30/68 (44%)
Query: 1 MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
+ A G +R+ R + LE F + +A +L L + +++WF NRR
Sbjct: 93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQ 152
Query: 61 KLKKEIQA 68
K K+ A
Sbjct: 153 KEKRMTPA 160
>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 = 68.1 bits (166), Expect = 2e-16
Identities = 19/64 (29%), Positives = 34/64 (53%)
Query: 1 MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
+GAN +R+ R T + LE+ F + + + + MA L L + +++WF NRR
Sbjct: 81 VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ 140
Query: 61 KLKK 64
+ K+
Sbjct: 141 REKR 144
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 65.1 bits (159), Expect = 6e-16
Identities = 10/57 (17%), Positives = 22/57 (38%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
+ + Q L+ F N + + + L+ R+++ WF +RR +
Sbjct: 9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRN 65
>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 = 63.5 bits (155), Expect = 2e-15
Identities = 20/59 (33%), Positives = 28/59 (47%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
R R +T YQ L+ F N Y ++++ L L R I +WFQN R K +K
Sbjct: 7 GRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65
>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 = 61.0 bits (148), Expect = 4e-14
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
+R R T T Q L +++ + TR+ +AH + L +R +++WFQN R + +K
Sbjct: 17 DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>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 = 62.0 bits (150), Expect = 7e-14
Identities = 19/63 (30%), Positives = 27/63 (42%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
G +R+ R ++T L F N T + EMA L +++WF NRR
Sbjct: 88 GEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQT 147
Query: 62 LKK 64
LK
Sbjct: 148 LKN 150
>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 = 59.7 bits (144), Expect = 6e-13
Identities = 16/64 (25%), Positives = 29/64 (45%)
Query: 1 MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 60
R+R R + LE F + + ++ +A+ L L + +++WF NRR
Sbjct: 90 ETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQ 149
Query: 61 KLKK 64
K K+
Sbjct: 150 KGKR 153
>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 = 57.0 bits (138), Expect = 1e-12
Identities = 17/61 (27%), Positives = 27/61 (44%)
Query: 4 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
+R R T Q L + F N+ + + EMA L ++ IK WF+N K +
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKER 63
Query: 64 K 64
+
Sbjct: 64 Q 64
>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 = 55.2 bits (133), Expect = 5e-12
Identities = 16/59 (27%), Positives = 31/59 (52%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
+R R ++ +Q ++ F NH + ++A LT+R +++WFQN R K ++
Sbjct: 7 GKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN 65
>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 = 54.2 bits (131), Expect = 1e-11
Identities = 24/58 (41%), Positives = 31/58 (53%)
Query: 8 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
RR R +T+ Q LE F N Y ++A L L +I+IWFQNRR KLK+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59
>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 = 54.7 bits (132), Expect = 1e-11
Identities = 25/59 (42%), Positives = 36/59 (61%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
+RR R T++ Q ELE+ F Y R E+A LTE +I++WFQNRR +L+K+
Sbjct: 18 QRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
>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 = 54.3 bits (131), Expect = 1e-11
Identities = 22/59 (37%), Positives = 33/59 (55%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
RR R T+TR Q LE F Y R E+A + L E ++++WF+NRR K +++
Sbjct: 7 GRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ 65
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 53.9 bits (130), Expect = 2e-11
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 10/82 (12%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
+R R ++T+ Q LEKEF HY R +A + L E +I++WF NRR K ++
Sbjct: 7 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR-- 64
Query: 67 QAIKELNEQEKQAQAQKAAAAA 88
+EK ++ + +
Sbjct: 65 --------EEKLRNQRRQSGPS 78
>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 = 53.9 bits (130), Expect = 2e-11
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 5 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
G +RR R +T Q +LE F N Y R E+A LTE ++++WF+NRR K +K
Sbjct: 1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 65 E 65
Sbjct: 61 R 61
>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 = 53.7 bits (129), Expect = 2e-11
Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 1/59 (1%)
Query: 7 RRRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
R R + L+ H Y + ++ L L + I +FQN+R +K
Sbjct: 7 GPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65
>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 = 52.7 bits (127), Expect = 4e-11
Identities = 19/59 (32%), Positives = 30/59 (50%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
RR R +T Q LE F Y R ++A + L E ++++WF+NRR K ++
Sbjct: 7 GRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65
>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 = 53.4 bits (128), Expect = 4e-11
Identities = 15/61 (24%), Positives = 25/61 (40%)
Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70
+ T+ Q LE F + + T+ + L+ R+I WF RR QA+
Sbjct: 17 FKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVL 76
Query: 71 E 71
+
Sbjct: 77 D 77
>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 = 52.4 bits (126), Expect = 5e-11
Identities = 17/64 (26%), Positives = 26/64 (40%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
R R Q L + N + ++ L+ R I++WFQN+R K KK
Sbjct: 3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62
Query: 67 QAIK 70
+K
Sbjct: 63 IMMK 66
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 52.4 bits (126), Expect = 5e-11
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 6 LRRRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
+ + T Q LE F+ N + +A LTE Q + WF+ R + ++
Sbjct: 1 MSAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRR 60
Query: 65 E 65
Sbjct: 61 S 61
>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 = 51.3 bits (123), Expect = 1e-10
Identities = 12/63 (19%), Positives = 23/63 (36%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
+ T+ Q L+ F + + + L +IK WF + R + ++ I
Sbjct: 4 HHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI 63
Query: 67 QAI 69
I
Sbjct: 64 VHI 66
>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 = 51.1 bits (123), Expect = 2e-10
Identities = 25/55 (45%), Positives = 34/55 (61%)
Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
T+T +Q ELEK F HY R E+A + LTE +I++WFQNRR K +K+
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>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 = 50.8 bits (121), Expect = 5e-10
Identities = 12/60 (20%), Positives = 23/60 (38%)
Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 70
+ T Q L+ F + LT + LT R+I WF ++ + + ++
Sbjct: 15 FKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKME 74
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 51.8 bits (123), Expect = 8e-10
Identities = 12/58 (20%), Positives = 23/58 (39%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
++ R +T Q L F N ++ +I ++ L L + +F N R +
Sbjct: 97 PKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLD 154
>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 = 49.6 bits (118), Expect = 1e-09
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 15/73 (20%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------LTERQI 51
R R T+ + +E F+ N Y +R E+A+A +T ++
Sbjct: 7 GRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKV 66
Query: 52 KIWFQNRRMKLKK 64
WF NRR ++K+
Sbjct: 67 YNWFANRRKEIKR 79
>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 = 48.7 bits (116), Expect = 2e-09
Identities = 14/55 (25%), Positives = 19/55 (34%)
Query: 11 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
+ Q LE F N + +T R+I WF RR K+ E
Sbjct: 11 YKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE 65
>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 = 45.2 bits (107), Expect = 3e-08
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 5 GLRRRGRQTYTRYQTLELEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
G++ LEK F Y +R ++ L + R+I+ WF++RR + K
Sbjct: 8 GIKDSPVNKVE--PNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
Query: 64 KEIQA 68
+
Sbjct: 66 PSGPS 70
>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 = 44.7 bits (106), Expect = 5e-08
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 8 RRGRQTYTRYQTLELEKEFH-TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
G T T Q LE F+ N + +A LTE Q + WF+ R + ++
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 43.1 bits (100), Expect = 2e-06
Identities = 13/83 (15%), Positives = 23/83 (27%), Gaps = 21/83 (25%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------- 45
N RR R + L + + ++ R +
Sbjct: 137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHG 196
Query: 46 -----LTERQIKIWFQNRRMKLK 63
+TE ++ WF NRR +
Sbjct: 197 LGSNLVTEVRVYNWFANRRKEEA 219
>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 = 38.7 bits (89), Expect = 2e-05
Identities = 11/63 (17%), Positives = 25/63 (39%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
G++G LE+ + + L +++ A L+ +Q+ WF +R +
Sbjct: 1 GSSGSSGPLPIPPPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQ 60
Query: 62 LKK 64
+
Sbjct: 61 PAE 63
>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 = 38.6 bits (89), Expect = 2e-05
Identities = 11/58 (18%), Positives = 17/58 (29%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
T Q L+ F + + ++A L I WF + R K
Sbjct: 25 STGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82
>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 = 37.9 bits (88), Expect = 2e-05
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 22 LEKEF-HTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
LEK F + +R ++ L R I+ WF+ RR + K
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58
>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 = 39.5 bits (91), Expect = 3e-05
Identities = 12/78 (15%), Positives = 22/78 (28%), Gaps = 21/78 (26%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC--------------------- 45
RR R + L + + ++ R +
Sbjct: 115 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 174
Query: 46 LTERQIKIWFQNRRMKLK 63
+TE ++ WF NRR +
Sbjct: 175 VTEVRVYNWFANRRKEEA 192
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 34.8 bits (79), Expect = 8e-04
Identities = 12/83 (14%), Positives = 23/83 (27%), Gaps = 21/83 (25%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC--------------------- 45
RR R + L + + ++ R +
Sbjct: 9 GRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNL 68
Query: 46 LTERQIKIWFQNRRMKLKKEIQA 68
+TE ++ WF NRR + +
Sbjct: 69 VTEVRVYNWFANRRKEEAFRHKL 91
>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 = 34.0 bits (77), Expect = 0.001
Identities = 10/60 (16%), Positives = 25/60 (41%), Gaps = 1/60 (1%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 61
G++G + L+ + N ++++ A+ L + +K WF+ R++
Sbjct: 1 GSSG-SSGSPINPYKDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY 59
>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 = 34.5 bits (78), Expect = 0.002
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 65 EIQAIKELNEQEKQAQAQKAAAAALAAA 92
E QA+K+L K A A A+ A
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKAT 45
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 32.3 bits (73), Expect = 0.003
Identities = 7/43 (16%), Positives = 17/43 (39%)
Query: 22 LEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
L+ + N + ++A ++ L +K WF+ +
Sbjct: 18 LKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60
>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 = 32.3 bits (73), Expect = 0.004
Identities = 12/50 (24%), Positives = 19/50 (38%)
Query: 15 TRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
T+ Q L+ F + R ++ L +I WF + R LK
Sbjct: 11 TKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 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 = 30.5 bits (69), Expect = 0.019
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 27 HTNH-YLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 65
+ + YL + + L+ QIK W RR K K
Sbjct: 24 NIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTI 63
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 31.6 bits (71), Expect = 0.026
Identities = 17/102 (16%), Positives = 32/102 (31%), Gaps = 24/102 (23%)
Query: 9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK-EI- 66
+G++ Y + E + + + E + E F++ + L +
Sbjct: 1680 KGKRIRENYSAMIFE------TIVDGKLKTEKIFKE-INEHSTSYTFRSEKGLLSATQFT 1732
Query: 67 Q--------AIKELNEQEKQAQAQKAAA-------AALAAAA 93
Q A E + + A A AALA+ A
Sbjct: 1733 QPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLA 1774
Score = 28.1 bits (62), Expect = 0.39
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 29/70 (41%)
Query: 21 ELEKE-FHTNHYLTRRRRIEMA-----------------HALCLTER---------QIKI 53
+++ TN +L +++E++ + L LT R Q +I
Sbjct: 348 QVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRI 407
Query: 54 WFQNRRMKLK 63
F R KLK
Sbjct: 408 PFSER--KLK 415
>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 = 29.6 bits (67), Expect = 0.031
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 27 HTNH-YLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
+ + YL + + L+ QIK W NRR K K
Sbjct: 20 NIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>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 = 29.4 bits (66), Expect = 0.054
Identities = 18/66 (27%), Positives = 24/66 (36%), Gaps = 3/66 (4%)
Query: 1 MGANGLRRRGRQTYTRYQTLELEKEFHTNH---YLTRRRRIEMAHALCLTERQIKIWFQN 57
M + +T+ LE F N YL + + L+ QIK W N
Sbjct: 21 MINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSN 80
Query: 58 RRMKLK 63
RR K K
Sbjct: 81 RRRKEK 86
>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 = 29.8 bits (67), Expect = 0.088
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 23 EKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 63
E+ F L + + E+A +T Q+++WF N+RM+ K
Sbjct: 381 EQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 29.0 bits (65), Expect = 0.093
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 27 HTNH-YLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAA 85
H ++ Y + + E+A +T Q+ WF N+R++ KK I +E A A
Sbjct: 23 HLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTAT 82
Query: 86 AAA 88
+
Sbjct: 83 NVS 85
>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Arabidopsis thaliana} SCOP:
a.4.1.1
Length = 80
Score = 28.8 bits (64), Expect = 0.11
Identities = 10/67 (14%), Positives = 22/67 (32%), Gaps = 4/67 (5%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC----LTERQIKIWFQN 57
+ G +R R +T Q ++ + ++ C + + +KIW N
Sbjct: 12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHN 71
Query: 58 RRMKLKK 64
+
Sbjct: 72 NKNSGPS 78
>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A
{Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*
Length = 995
Score = 28.9 bits (65), Expect = 0.21
Identities = 4/85 (4%), Positives = 23/85 (27%)
Query: 9 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 68
+ Y + + +E + + ++ N ++
Sbjct: 798 NAHKEYKKTEKPPKGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEK 857
Query: 69 IKELNEQEKQAQAQKAAAAALAAAA 93
++ + + + + ++ A+
Sbjct: 858 AEQEHAEALRIELKRQKKIAVLLQK 882
>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 = 26.9 bits (59), Expect = 0.24
Identities = 15/18 (83%), Positives = 16/18 (88%)
Query: 49 RQIKIWFQNRRMKLKKEI 66
RQIKIWFQNRRMK KK +
Sbjct: 1 RQIKIWFQNRRMKWKKRV 18
>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 = 26.8 bits (58), Expect = 0.52
Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 4/63 (6%)
Query: 7 RRRGRQTYTRYQTLELEKEFH----TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 62
+ R ++ L+K + + + R + +A L + ++ W NRR K
Sbjct: 8 ALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKY 67
Query: 63 KKE 65
+
Sbjct: 68 RLM 70
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 27.3 bits (59), Expect = 0.82
Identities = 10/78 (12%), Positives = 29/78 (37%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
R RGR ++ L + + M ++ + + F+ + + ++
Sbjct: 499 RGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHE 558
Query: 67 QAIKELNEQEKQAQAQKA 84
+ I++ E+ K ++
Sbjct: 559 KFIRDSQEKPKPVPDKEN 576
>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 = 26.7 bits (58), Expect = 1.2
Identities = 12/63 (19%), Positives = 23/63 (36%), Gaps = 6/63 (9%)
Query: 14 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELN 73
+ +T + + T Y+ +R R L + + +R K QA+ EL
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDR------LYNDNQVFAKYNVSRLQPYLKLRQALLELR 148
Query: 74 EQE 76
+
Sbjct: 149 PAK 151
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 25.0 bits (55), Expect = 2.1
Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 27 HTNH-YLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
H H Y + ++ ++A LT Q+ WF N R ++ + +
Sbjct: 20 HLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPM 60
>3r8s_H 50S ribosomal protein L9; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_F 1p86_F 1vs8_H 1vs6_H 2aw4_H 2awb_H 2gya_F 2gyc_F
1vt2_H 2i2v_H 2j28_H 2i2t_H* 2qao_H* 2qba_H* 2qbc_H*
2qbe_H 2qbg_H 2qbi_H* 2qbk_H* 2qov_H ...
Length = 149
Score = 25.3 bits (56), Expect = 3.4
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 63 KKEIQAIKELNEQEKQAQAQKAAAAALAAA 92
+ +A + E E + AAA A A
Sbjct: 44 IEFFEARRA--ELEAKLAEVLAAANARAEK 71
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 64
Score = 24.2 bits (53), Expect = 3.5
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 27 HTNH-YLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 64
H ++ Y + + E+A +T Q+ WF N+R++ KK
Sbjct: 25 HLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>3cb6_A FACT complex subunit SPT16; peptidase homology domain, histone
binding module, histone H chaperone, PITA-bread fold;
1.84A {Schizosaccharomyces pombe} PDB: 3cb5_A
Length = 444
Score = 25.3 bits (55), Expect = 3.7
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 64 KEIQAIKELNEQEKQAQAQKAAAAALAAAAVDH 96
+ AIK+ E A + + A ++ VD
Sbjct: 172 AKCLAIKDEQELANIKGASRVSVAVMSKYFVDE 204
>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 = 24.2 bits (53), Expect = 3.7
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 27 HTNH-YLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKE 71
H ++ Y + + E+A +T Q+ WF N+R++ KK I +E
Sbjct: 23 HLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQE 68
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 25.2 bits (54), Expect = 3.8
Identities = 7/65 (10%), Positives = 23/65 (35%)
Query: 7 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 66
R RGR ++ L + + M ++ + ++ F +++
Sbjct: 490 RGRGRARDSKCFLLTSSADVIEKEKANMIKEKIMNESILRLQTWDEMKFGKTVHRIQVNE 549
Query: 67 QAIKE 71
+ +++
Sbjct: 550 KLLRD 554
>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 = 24.8 bits (53), Expect = 3.9
Identities = 13/79 (16%), Positives = 24/79 (30%), Gaps = 21/79 (26%)
Query: 2 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALC---------------- 45
G++G R R + L + + ++ R +
Sbjct: 1 GSSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHG 60
Query: 46 -----LTERQIKIWFQNRR 59
+TE ++ WF NRR
Sbjct: 61 LGSNLVTEVRVYNWFANRR 79
>3f0n_A Mevalonate pyrophosphate decarboxylase; cholesterol biosynthesis,
lipid synthesis, lyase, steroid biosynthesis, sterol
biosynthesis; 1.90A {Mus musculus} PDB: 3d4j_A
Length = 414
Score = 25.2 bits (54), Expect = 3.9
Identities = 8/42 (19%), Positives = 14/42 (33%), Gaps = 3/42 (7%)
Query: 40 MAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQA 81
HA CL + + ++ IQ + N Q +
Sbjct: 276 QFHATCLDTFPPISYLNDTSRRI---IQLVHRFNTHHGQTKV 314
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.1 bits (54), Expect = 3.9
Identities = 8/36 (22%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 50 QIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAA 85
I+ W R + +K +Q + ++ +Q +KA
Sbjct: 86 SIRKW----REEQRKRLQELDAASKVMEQEWREKAK 117
Score = 24.3 bits (52), Expect = 8.3
Identities = 7/38 (18%), Positives = 15/38 (39%)
Query: 56 QNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAALAAAA 93
++ M+ + +A K+L E ++ Q A
Sbjct: 104 ASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIA 141
>3i1i_A Homoserine O-acetyltransferase; structural genomics, IDP01610,
O-acetyltransfera bacillus anthracis; HET: MSE; 2.44A
{Bacillus anthracis str}
Length = 377
Score = 25.3 bits (56), Expect = 4.0
Identities = 4/43 (9%), Positives = 10/43 (23%), Gaps = 10/43 (23%)
Query: 12 QTYTRYQTLELEKEFHTNHYL--TR--------RRRIEMAHAL 44
+ T + N ++ + + AL
Sbjct: 261 EKEINKLTYRSIELVDANSWMYTAKAVLLHDIAHGFSSLEEAL 303
>3bbo_J Ribosomal protein L9; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 197
Score = 25.1 bits (55), Expect = 4.1
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 63 KKEIQAIKELNEQEKQAQAQKAAAAALAAA 92
KE++ E E + Q K A LA
Sbjct: 93 LKELKMEDE--RIEAEKQRVKEEAQQLAMV 120
>3v2d_I 50S ribosomal protein L9; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus}
PDB: 2j03_I 2jl6_I 2jl8_I 2v47_I 2v49_I 2wdi_I 2wdj_I
2wdl_I 2wdn_I 2wh2_I 2x9s_I 2x9u_I 2xg0_I 2xg2_I 3hux_I
3huz_I 3i8f_K 3i8i_K 3i9c_K 3i9e_K ...
Length = 148
Score = 24.4 bits (54), Expect = 5.3
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 63 KKEIQAIKELNEQEKQAQAQKAAAAALAAA 92
K ++A Q K+ +KA A L
Sbjct: 44 LKALEARIR--AQAKRLAERKAEAERLKEI 71
>2jl6_1 50S ribosomal protein L28, 50S ribosomal protein L25;
methylation, translation, paromomycin, tRNA-binding,
tRNA, zinc, mRNA, ribosome, repressor, RNA-binding;
3.45A {Thermus thermophilus} PDB: 2jl8_1
Length = 89
Score = 24.2 bits (52), Expect = 6.3
Identities = 11/42 (26%), Positives = 22/42 (52%)
Query: 50 QIKIWFQNRRMKLKKEIQAIKELNEQEKQAQAQKAAAAALAA 91
++++ + + + I ++ E ++A A AAAAA AA
Sbjct: 48 KVRVRVAGQEITFRVAASHIPKVYELVERAAAAAAAAAAAAA 89
>4g6c_A Beta-hexosaminidase 1; ssgcid, niaid, structural genomics, Na
institute of allergy and infectious diseases; 1.38A
{Burkholderia cenocepacia}
Length = 342
Score = 24.5 bits (54), Expect = 6.9
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 58 RRMKLKKEIQAIKELNEQEKQAQAQKAAAAALA 90
+RM+ + + +L Q + QAQ ++ALA
Sbjct: 310 KRMRARGKALKWDKLIAQPEYLQAQALLSSALA 342
>1qam_A ERMC' methyltransferase; rRNA methyltransferase ERMC', cofactor
analogs; 2.20A {Bacillus subtilis} SCOP: c.66.1.24 PDB:
1qan_A* 1qao_A* 1qaq_A* 2erc_A
Length = 244
Score = 24.4 bits (54), Expect = 6.9
Identities = 4/27 (14%), Positives = 7/27 (25%)
Query: 48 ERQIKIWFQNRRMKLKKEIQAIKELNE 74
+ W K+ + Q L
Sbjct: 192 NYFVMKWVNKEYKKIFTKNQFNNSLKH 218
>2ivd_A PPO, PPOX, protoporphyrinogen oxidase; porphyrin biosynthesis,
chlorophyll biosynthesis, oxidoreductase, HAEM
biosynthesis, heme biosynthesis; HET: ACJ FAD TWN; 2.3A
{Myxococcus xanthus} SCOP: c.3.1.2 d.16.1.5 PDB: 2ive_A*
Length = 478
Score = 24.6 bits (53), Expect = 7.5
Identities = 9/38 (23%), Positives = 11/38 (28%)
Query: 1 MGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRI 38
G N R T L LE +RR +
Sbjct: 67 QGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYV 104
>1nkw_F 50S ribosomal protein L9; ribosome, large subunit, X- RAY
structure, peptidyl-transferase, peptide bond
formation; 3.10A {Deinococcus radiodurans} SCOP:
i.1.1.2 PDB: 1nwx_F* 1nwy_F* 1sm1_F* 1xbp_F* 1pnu_F
1pny_F 1vor_I 1vou_I 1vow_I 1voy_I 1vp0_I
Length = 146
Score = 24.1 bits (53), Expect = 8.1
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 2/30 (6%)
Query: 63 KKEIQAIKELNEQEKQAQAQKAAAAALAAA 92
K ++A EK+ +KA A LA+
Sbjct: 43 MKTLEAQLR--SIEKRQAQEKAVAEDLASR 70
>1div_A Ribosomal protein L9; rRNA-binding; 2.60A {Geobacillus
stearothermophilus} SCOP: d.99.1.1 d.100.1.1 PDB:
1giy_K 1yl3_K 2b66_I 2b9n_I 2b9p_I 487d_K
Length = 149
Score = 24.1 bits (53), Expect = 8.9
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 63 KKEIQAIKELNEQEKQAQAQKAAAAALAAA 92
K ++A K+ ++++QA + A A L
Sbjct: 44 LKALEAQKQ--KEQRQAAEELANAKKLKEQ 71
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
0.321 0.128 0.359
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,509,641
Number of extensions: 80193
Number of successful extensions: 518
Number of sequences better than 10.0: 1
Number of HSP's gapped: 499
Number of HSP's successfully gapped: 137
Length of query: 96
Length of database: 6,701,793
Length adjustment: 62
Effective length of query: 34
Effective length of database: 4,970,691
Effective search space: 169003494
Effective search space used: 169003494
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.4 bits)