Query 000281
Match_columns 1728
No_of_seqs 623 out of 2815
Neff 5.4
Searched_HMMs 29240
Date Tue Mar 26 16:00:37 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000281.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_61-64//hhsearch_pdb/000281hhsearch_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 1 124.8 3.0 65 29-93 96-160 (164)
2 2kt0_A Nanog, homeobox protein 1.0 1 1 122.0 6.3 66 28-93 18-83 (84)
3 2dmt_A Homeobox protein BARH-l 1.0 1 1 121.9 6.1 65 28-92 13-77 (80)
4 1e3o_C Octamer-binding transcr 1.0 1 1 121.5 3.5 61 30-90 99-159 (160)
5 2cue_A Paired box protein PAX6 1.0 1 1 121.2 4.4 67 28-94 3-69 (80)
6 1au7_A Protein PIT-1, GHF-1; c 1.0 1 1 120.8 3.6 63 29-91 84-146 (146)
7 2dms_A Homeobox protein OTX2; 1.0 1 1 120.6 6.1 66 28-93 3-68 (80)
8 3a01_A Homeodomain-containing 1.0 1 1 120.5 5.5 69 29-97 14-82 (93)
9 1wh5_A ZF-HD homeobox family p 1.0 1 1 120.3 5.3 61 29-89 14-78 (80)
10 2cra_A Homeobox protein HOX-B1 1.0 1 1 120.3 5.2 65 28-92 3-67 (70)
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=124.76 Aligned_cols=65 Identities=25% Similarity=0.396 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHCCC
Q ss_conf 99999998758978999999988325999988899999982999555001144200222110149
Q 000281 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKEN 93 (1728)
Q Consensus 29 ~~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~~~~ 93 (1728)
.+++|++||.|+..|+..|+..|..++||+...+..||..++|+++||+|||||||+|+||....
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=121.97 Aligned_cols=66 Identities=29% Similarity=0.418 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHCCC
Q ss_conf 899999998758978999999988325999988899999982999555001144200222110149
Q 000281 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKEN 93 (1728)
Q Consensus 28 ~~~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~~~~ 93 (1728)
...+.++.||.|+..|+..|+..|..++||+...+..||..|||+++||+|||||||+|+|+.++.
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
>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=121.86 Aligned_cols=65 Identities=37% Similarity=0.609 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHCC
Q ss_conf 89999999875897899999998832599998889999998299955500114420022211014
Q 000281 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1728)
Q Consensus 28 ~~~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~~~ 92 (1728)
..++.++.||.||..|+..|+..|..++||+...+..||..|+|+++||+|||||||+|+|+...
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 4
>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=121.54 Aligned_cols=61 Identities=23% Similarity=0.438 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHH
Q ss_conf 9999998758978999999988325999988899999982999555001144200222110
Q 000281 30 QQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKE 90 (1728)
Q Consensus 30 ~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~ 90 (1728)
.++|++||.|+..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+||.
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 5
>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=121.22 Aligned_cols=67 Identities=33% Similarity=0.588 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHCCCC
Q ss_conf 8999999987589789999999883259999888999999829995550011442002221101499
Q 000281 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKENP 94 (1728)
Q Consensus 28 ~~~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~~~~~ 94 (1728)
.+...++.||.||..|+..|+..|..++||+...+..||..|+|++++|+|||||||+|+|+.....
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 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=120.82 Aligned_cols=63 Identities=24% Similarity=0.558 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHC
Q ss_conf 999999987589789999999883259999888999999829995550011442002221101
Q 000281 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEK 91 (1728)
Q Consensus 29 ~~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~~ 91 (1728)
.+++|++||.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+||++
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
>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=120.58 Aligned_cols=66 Identities=32% Similarity=0.588 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHCCC
Q ss_conf 899999998758978999999988325999988899999982999555001144200222110149
Q 000281 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKEN 93 (1728)
Q Consensus 28 ~~~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~~~~ 93 (1728)
.+++.++.|+.||..|+..|+..|..++||+...+..||..++|++++|+|||||||+|+|+....
T Consensus 3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~ 68 (80)
T 2dms_A 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQ 68 (80)
T ss_dssp CCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCS
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 999999899989999999999999725997999999999997939899124138775775698771
No 8
>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=120.46 Aligned_cols=69 Identities=28% Similarity=0.454 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHCCCCCCC
Q ss_conf 999999987589789999999883259999888999999829995550011442002221101499843
Q 000281 29 GQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKENPPKK 97 (1728)
Q Consensus 29 ~~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~~~~~~~q 97 (1728)
..+.++.||.||..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+|+........
T Consensus 14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~ 82 (93)
T 3a01_A 14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREA 82 (93)
T ss_dssp CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC---
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 988898996879999999999997079969999999999949795435141175520335653788789
No 9
>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=120.33 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=58.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHH----CCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHH
Q ss_conf 9999999875897899999998832----599998889999998299955500114420022211
Q 000281 29 GQQGKPKRQMKTPFQLETLEKAYAS----ETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKK 89 (1728)
Q Consensus 29 ~~k~kr~Rt~fT~~Ql~~LE~~F~~----~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr 89 (1728)
.+++||.||.||..|+..|+..|+. ++||+...+.+||..|+|+++||+|||||||+|+|+
T Consensus 14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~ 78 (80)
T 1wh5_A 14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS 78 (80)
T ss_dssp CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 78889898357999999999999854676889499999999999598934313776145767778
No 10
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1
Probab=1.00 E-value=1 Score=120.32 Aligned_cols=65 Identities=35% Similarity=0.622 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHCC
Q ss_conf 89999999875897899999998832599998889999998299955500114420022211014
Q 000281 28 EGQQGKPKRQMKTPFQLETLEKAYASETYPSESTRAELSEKLGLSDRQLQMWFCHRRLKDKKEKE 92 (1728)
Q Consensus 28 ~~~k~kr~Rt~fT~~Ql~~LE~~F~~~~yPs~~~R~~LA~~LgLterqVqVWFQNRRaK~Kr~~~ 92 (1728)
.+++.+++|+.||..|+..|+..|..++||+...+..||..++|+++||+|||||||+|+|+...
T Consensus 3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~ 67 (70)
T 2cra_A 3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67 (70)
T ss_dssp SSCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf 99999989986899999999999970599899999999999798889914864757778612477
Done!