Query 000279
Match_columns 1729
No_of_seqs 613 out of 2810
Neff 5.4
Searched_HMMs 29240
Date Tue Mar 26 18:21:21 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000279.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_56-60//hhsearch_pdb/000279hhsearch_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 64 29-92 96-159 (164)
2 1e3o_C Octamer-binding transcr 1.0 1 1 122.4 3.3 61 30-90 99-159 (160)
3 2kt0_A Nanog, homeobox protein 1.0 1 1 122.1 6.2 64 29-92 19-82 (84)
4 2dmt_A Homeobox protein BARH-l 1.0 1 1 121.9 6.0 65 28-92 13-77 (80)
5 3a01_A Homeodomain-containing 1.0 1 1 121.7 5.0 70 30-99 15-84 (93)
6 1wh5_A ZF-HD homeobox family p 1.0 1 1 121.3 5.2 62 28-89 13-78 (80)
7 1au7_A Protein PIT-1, GHF-1; c 1.0 1 1 121.3 3.5 63 29-91 84-146 (146)
8 2cue_A Paired box protein PAX6 1.0 1 1 121.1 4.3 67 28-94 3-69 (80)
9 1wh7_A ZF-HD homeobox family p 1.0 1 1 120.9 4.9 62 27-89 12-78 (80)
10 2da3_A Alpha-fetoprotein enhan 1.0 1 1 120.8 5.0 65 28-92 13-77 (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=124.57 Aligned_cols=64 Identities=25% Similarity=0.404 Sum_probs=60.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCC
Q ss_conf 9999999875897899999997842499998999999999299966511114531022111014
Q 000279 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1729)
Q Consensus 29 ~~k~Kr~Rt~fT~~Ql~~Le~~F~~~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR~~~ 92 (1729)
..++|++||.|+..|+..|+..|..++||+...|.+||..++|+++||+|||||||+|+||...
T Consensus 96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~ 159 (164)
T 2xsd_C 96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTP 159 (164)
T ss_dssp ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC
T ss_pred CCCCCCCCEECCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 6668988530469999999999804899999999999999797854421662776577762247
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=122.38 Aligned_cols=61 Identities=23% Similarity=0.438 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHC
Q ss_conf 9999998758978999999978424999989999999992999665111145310221110
Q 000279 30 QQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKE 90 (1729)
Q Consensus 30 ~k~Kr~Rt~fT~~Ql~~Le~~F~~~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR~ 90 (1729)
.++|++||.|+..|+..|+..|..++||+...|..||..+||+++||+|||||||+|+||+
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=122.10 Aligned_cols=64 Identities=28% Similarity=0.421 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCC
Q ss_conf 9999999875897899999997842499998999999999299966511114531022111014
Q 000279 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1729)
Q Consensus 29 ~~k~Kr~Rt~fT~~Ql~~Le~~F~~~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR~~~ 92 (1729)
..+.++.||.|+..|+.+|+..|..++||+...+..||..+||+++||+|||||||+|+|+...
T Consensus 19 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k 82 (84)
T 2kt0_A 19 PVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82 (84)
T ss_dssp CSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCC
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 8899989988899999999999980799899999999999399899989999999998877750
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=121.92 Aligned_cols=65 Identities=37% Similarity=0.609 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCC
Q ss_conf 89999999875897899999997842499998999999999299966511114531022111014
Q 000279 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1729)
Q Consensus 28 ~~~k~Kr~Rt~fT~~Ql~~Le~~F~~~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR~~~ 92 (1729)
..++.++.||.||..|+.+|+..|..++||+...+..||..|+|+++||+|||||||+|+|+...
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
>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=121.66 Aligned_cols=70 Identities=29% Similarity=0.468 Sum_probs=63.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCCCCCCCCC
Q ss_conf 9999998758978999999978424999989999999992999665111145310221110149984334
Q 000279 30 QQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKENPPKKMR 99 (1729)
Q Consensus 30 ~k~Kr~Rt~fT~~Ql~~Le~~F~~~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR~~~~~~~q~~ 99 (1729)
.+.+++||.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+|+..........
T Consensus 15 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~~~ 84 (93)
T 3a01_A 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAER 84 (93)
T ss_dssp CCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC-----
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 8889899687999999999999707996999999999994979543514117552033565378878999
No 6
>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=121.31 Aligned_cols=62 Identities=15% Similarity=0.198 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHH
Q ss_conf 89999999875897899999997842----499998999999999299966511114531022111
Q 000279 28 EGQQGKPKRQMKTPFQLETLEKAYAS----ETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKK 89 (1729)
Q Consensus 28 ~~~k~Kr~Rt~fT~~Ql~~Le~~F~~----~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR 89 (1729)
...++||+||.||..|+..|+..|.. ++||+...|.+||..|+|+++||+|||||||+|+|+
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 7
>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=121.26 Aligned_cols=63 Identities=24% Similarity=0.558 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCC
Q ss_conf 999999987589789999999784249999899999999929996651111453102211101
Q 000279 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEK 91 (1729)
Q Consensus 29 ~~k~Kr~Rt~fT~~Ql~~Le~~F~~~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR~~ 91 (1729)
..++|++||.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+||++
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 8
>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=121.12 Aligned_cols=67 Identities=33% Similarity=0.588 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCCCC
Q ss_conf 8999999987589789999999784249999899999999929996651111453102211101499
Q 000279 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKENP 94 (1729)
Q Consensus 28 ~~~k~Kr~Rt~fT~~Ql~~Le~~F~~~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR~~~~~ 94 (1729)
.+...+++|+.||..|+.+|+..|..++||+...+..||..++|++++|+|||||||+|+|+.....
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 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=120.95 Aligned_cols=62 Identities=18% Similarity=0.259 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHH-----CCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHH
Q ss_conf 989999999875897899999997842-----499998999999999299966511114531022111
Q 000279 27 NEGQQGKPKRQMKTPFQLETLEKAYAS-----ETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKK 89 (1729)
Q Consensus 27 ~~~~k~Kr~Rt~fT~~Ql~~Le~~F~~-----~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR 89 (1729)
....++||.||.||..|+..|+ .|.. ++||+...|.+||..|+|+++||||||||||+|+|+
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
No 10
>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=120.83 Aligned_cols=65 Identities=31% Similarity=0.524 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHCCC
Q ss_conf 89999999875897899999997842499998999999999299966511114531022111014
Q 000279 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1729)
Q Consensus 28 ~~~k~Kr~Rt~fT~~Ql~~Le~~F~~~~yPs~~~R~eLA~~lgLserqVqVWFQNRRaK~RR~~~ 92 (1729)
...+.++.||.||..|+.+|+..|..++||+...+.+||..|+|+++||+|||||||+|+|+...
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
Done!