Query 000285
Match_columns 1722
No_of_seqs 619 out of 2803
Neff 5.4
Searched_HMMs 29240
Date Tue Mar 26 16:05:03 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000285.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_65-69//hhsearch_pdb/000285hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2xsd_C POU domain, class 3, tr 1.0 1 1 124.6 2.8 65 29-93 96-160 (164)
2 1e3o_C Octamer-binding transcr 1.0 1 1 121.6 3.4 61 30-90 99-159 (160)
3 2kt0_A Nanog, homeobox protein 1.0 1 1 121.5 6.4 66 28-93 18-83 (84)
4 2dmt_A Homeobox protein BARH-l 1.0 1 1 121.4 6.1 65 28-92 13-77 (80)
5 1au7_A Protein PIT-1, GHF-1; c 1.0 1 1 120.9 3.6 63 29-91 84-146 (146)
6 2cue_A Paired box protein PAX6 1.0 1 1 120.8 4.1 67 28-94 3-69 (80)
7 3a01_A Homeodomain-containing 1.0 1 1 120.5 5.3 70 28-97 13-82 (93)
8 1wh5_A ZF-HD homeobox family p 1.0 1 1 120.5 5.3 62 28-89 13-78 (80)
9 2dms_A Homeobox protein OTX2; 1.0 1 1 120.2 6.0 65 28-92 3-67 (80)
10 1wh7_A ZF-HD homeobox family p 1.0 1 1 120.2 4.9 62 27-89 12-78 (80)
No 1
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}
Probab=1.00 E-value=1 Score=124.56 Aligned_cols=65 Identities=25% Similarity=0.396 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCCC
Q ss_conf 99999998758978999999988425999988999999982999766101133100111000149
Q 000285 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKEN 93 (1722)
Q Consensus 29 ~~k~rr~RT~fT~~Ql~~Le~~F~~~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr~~~~ 93 (1722)
.+++|++||.|+..|+..|+..|..++||+...+..||..++|+++||+|||||||+|+||....
T Consensus 96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~ 160 (164)
T 2xsd_C 96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA 160 (164)
T ss_dssp ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred CCCCCCCCEECCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf 66689885304699999999998048999999999999997978544216627765777622478
No 2
>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
Probab=1.00 E-value=1 Score=121.62 Aligned_cols=61 Identities=23% Similarity=0.438 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHC
Q ss_conf 9999998758978999999988425999988999999982999766101133100111000
Q 000285 30 QQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKE 90 (1722)
Q Consensus 30 ~k~rr~RT~fT~~Ql~~Le~~F~~~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr~ 90 (1722)
.++|++||.|+..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+||.
T Consensus 99 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~ 159 (160)
T 1e3o_C 99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 159 (160)
T ss_dssp -----CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf 8888575236899999999998615999999999999997978677068508866002005
No 3
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=121.47 Aligned_cols=66 Identities=29% Similarity=0.418 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCCC
Q ss_conf 899999998758978999999988425999988999999982999766101133100111000149
Q 000285 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKEN 93 (1722)
Q Consensus 28 ~~~k~rr~RT~fT~~Ql~~Le~~F~~~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr~~~~ 93 (1722)
...+.++.||.|+..|+..|+..|..++||+...+..||..|||+++||+|||||||+|+|+..+.
T Consensus 18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k~ 83 (84)
T 2kt0_A 18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83 (84)
T ss_dssp CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCCC
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 888999899888999999999999807998999999999993998999899999999988777506
No 4
>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}
Probab=1.00 E-value=1 Score=121.45 Aligned_cols=65 Identities=37% Similarity=0.609 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCC
Q ss_conf 89999999875897899999998842599998899999998299976610113310011100014
Q 000285 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1722)
Q Consensus 28 ~~~k~rr~RT~fT~~Ql~~Le~~F~~~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr~~~ 92 (1722)
..++.++.||.||..|+..|+..|..++||+...+..||..|+|+++||+|||||||+|+|+...
T Consensus 13 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~ 77 (80)
T 2dmt_A 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77 (80)
T ss_dssp CCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHEEECCHHHHHHHHCCCC
T ss_conf 77889989988899999999999980699987999999999698889910161879887620068
No 5
>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
Probab=1.00 E-value=1 Score=120.87 Aligned_cols=63 Identities=24% Similarity=0.558 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCC
Q ss_conf 999999987589789999999884259999889999999829997661011331001110001
Q 000285 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEK 91 (1722)
Q Consensus 29 ~~k~rr~RT~fT~~Ql~~Le~~F~~~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr~~ 91 (1722)
.+++|++||.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+||.+
T Consensus 84 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~k 146 (146)
T 1au7_A 84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 146 (146)
T ss_dssp -----CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSCC
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHCCC
T ss_conf 777888876764999999999999769989999999999969884232042176654552159
No 6
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1
Probab=1.00 E-value=1 Score=120.76 Aligned_cols=67 Identities=33% Similarity=0.588 Sum_probs=61.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCCCC
Q ss_conf 8999999987589789999999884259999889999999829997661011331001110001499
Q 000285 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKENP 94 (1722)
Q Consensus 28 ~~~k~rr~RT~fT~~Ql~~Le~~F~~~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr~~~~~ 94 (1722)
++...++.||.||..|+..|+..|..++||+...+..||..|+|++++|+|||||||+|+|+.....
T Consensus 3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~ 69 (80)
T 2cue_A 3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR 69 (80)
T ss_dssp SCCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999998998469999999999986469989999999999829998993398899899998873653
No 7
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}
Probab=1.00 E-value=1 Score=120.45 Aligned_cols=70 Identities=27% Similarity=0.447 Sum_probs=62.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCCCCCCC
Q ss_conf 8999999987589789999999884259999889999999829997661011331001110001499843
Q 000285 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKENPPKK 97 (1722)
Q Consensus 28 ~~~k~rr~RT~fT~~Ql~~Le~~F~~~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr~~~~~~~~ 97 (1722)
...+.+++||.||..|+..|+..|..++||+...+..||..+||++++|+|||||||+|+|+........
T Consensus 13 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~ 82 (93)
T 3a01_A 13 TPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREA 82 (93)
T ss_dssp CCCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC---
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9988898996879999999999997079969999999999949795435141175520335653788789
No 8
>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
Probab=1.00 E-value=1 Score=120.45 Aligned_cols=62 Identities=15% Similarity=0.198 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHH
Q ss_conf 89999999875897899999998842----599998899999998299976610113310011100
Q 000285 28 EGQQGKPKRQMKTPFQLETLEKAYAS----ETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKK 89 (1722)
Q Consensus 28 ~~~k~rr~RT~fT~~Ql~~Le~~F~~----~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr 89 (1722)
..+++||.||.||..|+..|+..|.. ++||+...+.+||..|+|+++||+|||||||+|+|+
T Consensus 13 ~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~ 78 (80)
T 1wh5_A 13 GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS 78 (80)
T ss_dssp CCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 778889898357999999999999854676889499999999999598934313776145767778
No 9
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}
Probab=1.00 E-value=1 Score=120.21 Aligned_cols=65 Identities=32% Similarity=0.593 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCC
Q ss_conf 89999999875897899999998842599998899999998299976610113310011100014
Q 000285 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1722)
Q Consensus 28 ~~~k~rr~RT~fT~~Ql~~Le~~F~~~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr~~~ 92 (1722)
.+++.++.|+.||..|+..|+..|..++||+...+..||..|+|++++|+|||||||+|+|+...
T Consensus 3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~ 67 (80)
T 2dms_A 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67 (80)
T ss_dssp CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTC
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999989998999999999999972599799999999999793989912413877577569877
No 10
>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
Probab=1.00 E-value=1 Score=120.18 Aligned_cols=62 Identities=18% Similarity=0.259 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHH-----CCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHH
Q ss_conf 989999999875897899999998842-----599998899999998299976610113310011100
Q 000285 27 NEGQQGKPKRQMKTPFQLETLEKAYAS-----ETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKK 89 (1722)
Q Consensus 27 ~~~~k~rr~RT~fT~~Ql~~Le~~F~~-----~~yPs~~~R~~LA~~LgLserqVqVWFQNRRaK~Kr 89 (1722)
....++||.||.||..|+..|+ .|.. ++||+...+.+||..|+|+++||+|||||||+|+|+
T Consensus 12 ~~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~ 78 (80)
T 1wh7_A 12 SSGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS 78 (80)
T ss_dssp CCCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred CCCCCCCCCCCCCCHHHHHHHH-HHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 8888889898447999999999-999973767779899999999999596968333560022547778
Done!