Query 000448
Match_columns 1497
No_of_seqs 618 out of 3066
Neff 5.7
Searched_HMMs 29240
Date Tue Mar 26 17:20:24 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000448.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_225-229//hhsearch_pdb/000448hhsearch_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 1 122.4 4.3 65 29-93 96-160 (164)
2 2kt0_A Nanog, homeobox protein 1.0 1 1 121.7 7.7 66 28-93 18-83 (84)
3 1e3o_C Octamer-binding transcr 1.0 1 1 121.4 4.7 61 30-90 99-159 (160)
4 2dmt_A Homeobox protein BARH-l 1.0 1 1 120.9 7.4 65 28-92 13-77 (80)
5 1wh5_A ZF-HD homeobox family p 1.0 1 1 120.5 6.4 63 28-90 13-79 (80)
6 1au7_A Protein PIT-1, GHF-1; c 1.0 1 1 120.0 4.8 63 29-91 84-146 (146)
7 3a01_A Homeodomain-containing 1.0 1 1 119.9 6.5 71 29-99 14-84 (93)
8 2da3_A Alpha-fetoprotein enhan 1.0 1 1 119.7 6.3 65 28-92 13-77 (80)
9 1wh7_A ZF-HD homeobox family p 1.0 1 1 119.2 5.7 63 27-90 12-79 (80)
10 2cue_A Paired box protein PAX6 1.0 1 1 118.3 5.4 65 29-93 4-68 (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=122.39 Aligned_cols=65 Identities=25% Similarity=0.396 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf 99999998768988999999988423999999999999982999222100122002221110149
Q 000448 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKEN 93 (1497)
Q Consensus 29 ~~k~kr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~~~~ 93 (1497)
.+++|++||.||..|+..|+..|..++||+...|.+||..+||+++||+|||||||+|+||....
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
>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=121.70 Aligned_cols=66 Identities=29% Similarity=0.418 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf 899999998768988999999988423999999999999982999222100122002221110149
Q 000448 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKEN 93 (1497)
Q Consensus 28 ~~~k~kr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~~~~ 93 (1497)
...+.++.|+.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+|+....
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 3
>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=121.35 Aligned_cols=61 Identities=23% Similarity=0.438 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHC
Q ss_conf 9999998768988999999988423999999999999982999222100122002221110
Q 000448 30 QQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKE 90 (1497)
Q Consensus 30 ~k~kr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~ 90 (1497)
.++|++||.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+||.
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 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=120.86 Aligned_cols=65 Identities=37% Similarity=0.609 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCC
Q ss_conf 89999999876898899999998842399999999999998299922210012200222111014
Q 000448 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1497)
Q Consensus 28 ~~~k~kr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~~~ 92 (1497)
..++.++.|+.||..|+..|+..|..++||+...+.+||..+||+++||+|||||||+|+|+...
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
>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=120.49 Aligned_cols=63 Identities=14% Similarity=0.196 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHC
Q ss_conf 89999999876898899999998842----3999999999999982999222100122002221110
Q 000448 28 EGQQGKPKRQMKTPFQLETLEKAYAS----ETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKE 90 (1497)
Q Consensus 28 ~~~k~kr~Rt~ft~~Ql~~Le~~F~~----~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~ 90 (1497)
..+++||.||.||..|+..|+..|.. ++||+...+.+||..|||+++||+|||||||+|+|+.
T Consensus 13 ~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~~ 79 (80)
T 1wh5_A 13 GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPSS 79 (80)
T ss_dssp CCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSCC
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf 7788898983579999999999998546768894999999999995989343137761457677789
No 6
>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=120.00 Aligned_cols=63 Identities=24% Similarity=0.558 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCC
Q ss_conf 999999987689889999999884239999999999999829992221001220022211101
Q 000448 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEK 91 (1497)
Q Consensus 29 ~~k~kr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~~ 91 (1497)
.+++|++||.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+||.+
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 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=119.90 Aligned_cols=71 Identities=28% Similarity=0.454 Sum_probs=63.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCCCCCCC
Q ss_conf 99999998768988999999988423999999999999982999222100122002221110149985445
Q 000448 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKENPPKKMR 99 (1497)
Q Consensus 29 ~~k~kr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~~~~~~~~~~ 99 (1497)
..+.+++||.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+|+..........
T Consensus 14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~~~ 84 (93)
T 3a01_A 14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAER 84 (93)
T ss_dssp CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-----
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 98889899687999999999999707996999999999994979543514117552033565378878999
No 8
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=119.72 Aligned_cols=65 Identities=31% Similarity=0.524 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCC
Q ss_conf 89999999876898899999998842399999999999998299922210012200222111014
Q 000448 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1497)
Q Consensus 28 ~~~k~kr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~~~ 92 (1497)
...+.++.|+.||..|+..|+..|..++||+...+.+||..+||++.||+|||||||+|+|+...
T Consensus 13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 77 (80)
T 2da3_A 13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP 77 (80)
T ss_dssp CCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 88999989999899999999999982599999999999999795998968975877886713145
No 9
>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=119.25 Aligned_cols=63 Identities=17% Similarity=0.256 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHH-----CCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHC
Q ss_conf 989999999876898899999998842-----3999999999999982999222100122002221110
Q 000448 27 NEGQQGKPKRQMKTPFQLETLEKAYAS-----ETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKE 90 (1497)
Q Consensus 27 ~~~~k~kr~Rt~ft~~Ql~~Le~~F~~-----~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~ 90 (1497)
....++||.||.||..|+..|+ .|.. ++||+...|.+||..|||+++||+|||||||+|+|+.
T Consensus 12 ~~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~s 79 (80)
T 1wh7_A 12 SSGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS 79 (80)
T ss_dssp CCCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred CCCCCCCCCCCCCCHHHHHHHH-HHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf 8888889898447999999999-9999737677798999999999995969683335600225477789
No 10
>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=118.31 Aligned_cols=65 Identities=34% Similarity=0.609 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf 99999998768988999999988423999999999999982999222100122002221110149
Q 000448 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKEN 93 (1497)
Q Consensus 29 ~~k~kr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~eLA~~LgLs~~qVqvWFQNRRaK~Kr~~~~ 93 (1497)
+...++.|+.||..|+..|+..|..++||+...+..||..+||++.||+|||||||+|+|+....
T Consensus 4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~ 68 (80)
T 2cue_A 4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL 68 (80)
T ss_dssp CCSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999899846999999999998646998999999999982999899339889989999887365
Done!