Query 001512
Match_columns 1063
No_of_seqs 464 out of 2000
Neff 4.4
Searched_HMMs 29240
Date Tue Mar 26 17:31:55 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/001512.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_812-815//hhsearch_pdb/001512hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1e3o_C Octamer-binding transcr 1.0 1 1 119.4 3.1 62 881-945 99-160 (160)
2 2cue_A Paired box protein PAX6 1.0 1 1 118.8 2.0 69 880-951 4-72 (80)
3 2dmt_A Homeobox protein BARH-l 1.0 1 1 118.8 5.8 65 879-946 13-77 (80)
4 2xsd_C POU domain, class 3, tr 1.0 1 1 118.6 2.9 65 880-947 96-160 (164)
5 2dms_A Homeobox protein OTX2; 1.0 1 1 118.3 4.7 70 879-951 3-72 (80)
6 2dmq_A LIM/homeobox protein LH 1.0 1 1 118.1 3.0 69 879-950 3-71 (80)
7 2kt0_A Nanog, homeobox protein 1.0 1 1 118.0 6.8 66 879-947 18-83 (84)
8 1au7_A Protein PIT-1, GHF-1; c 1.0 1 1 117.2 3.4 63 880-945 84-146 (146)
9 2da3_A Alpha-fetoprotein enhan 1.0 1 1 117.0 4.3 65 879-946 13-77 (80)
10 3a01_A Homeodomain-containing 1.0 1 1 116.6 2.4 69 880-951 14-82 (93)
No 1
>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=119.37 Aligned_cols=62 Identities=32% Similarity=0.462 Sum_probs=57.6
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCC
Q ss_conf 99998974457985789999999764179999899999999939996541000333411127888
Q 001512 881 SRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPS 945 (1063)
Q Consensus 881 sk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~ 945 (1063)
.+.||.|+.|+ ..|+..|+..|..++||+...|..||..|||+++||+|||||||+|+||..
T Consensus 99 ~~~rr~Rt~ft---~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~ 160 (160)
T 1e3o_C 99 SRRRKKRTSIE---TNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 160 (160)
T ss_dssp -----CCCCCC---HHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSCC
T ss_pred CCCCCCCCCCC---HHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC
T ss_conf 88885752368---999999999986159999999999999979786770685088660020059
No 2
>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=118.80 Aligned_cols=69 Identities=29% Similarity=0.569 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 999998974457985789999999764179999899999999939996541000333411127888711001
Q 001512 880 GSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPSSKNAKL 951 (1063)
Q Consensus 880 gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~~~~~~~ 951 (1063)
+...+|.|+.|+ ..|+..|+..|..++||+...+..||..|+|++.||+|||||||+|+|+........
T Consensus 4 ~~~~rr~Rt~ft---~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~~~~ 72 (80)
T 2cue_A 4 GSSGQRNRTSFT---QEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQR 72 (80)
T ss_dssp CCSSCCCCCCSC---HHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCC---HHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 999998998469---999999999986469989999999999829998993398899899998873653234
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=118.79 Aligned_cols=65 Identities=29% Similarity=0.557 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCC
Q ss_conf 99999989744579857899999997641799998999999999399965410003334111278887
Q 001512 879 PGSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPSS 946 (1063)
Q Consensus 879 ~gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~~ 946 (1063)
..++.+|.|+.|+ ..|+..|+..|..++||+...++.||..|+|++.||+|||||||+|+|+...
T Consensus 13 ~~~~~rr~Rt~ft---~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~ 77 (80)
T 2dmt_A 13 KAKKGRRSRTVFT---ELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77 (80)
T ss_dssp CCCCCCCSCCCCC---HHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred CCCCCCCCCCCCC---HHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHEEECCHHHHHHHHCCCC
T ss_conf 7788998998889---9999999999980699987999999999698889910161879887620068
No 4
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}
Probab=1.00 E-value=1 Score=118.61 Aligned_cols=65 Identities=29% Similarity=0.337 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCC
Q ss_conf 99999897445798578999999976417999989999999993999654100033341112788871
Q 001512 880 GSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPSSK 947 (1063)
Q Consensus 880 gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~~~ 947 (1063)
..+.||.|+.|+ ..|+..|+..|..++||+...|..||..|+|+++||+|||||||+|+||....
T Consensus 96 ~~~~rr~Rt~ft---~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~ 160 (164)
T 2xsd_C 96 QGRKRKKRTSIE---VGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA 160 (164)
T ss_dssp ----------CC---HHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred CCCCCCCCEECC---HHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf 666898853046---99999999998048999999999999997978544216627765777622478
No 5
>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=118.32 Aligned_cols=70 Identities=29% Similarity=0.494 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 9999998974457985789999999764179999899999999939996541000333411127888711001
Q 001512 879 PGSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPSSKNAKL 951 (1063)
Q Consensus 879 ~gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~~~~~~~ 951 (1063)
.+++.+|.|+.|+ ..|+..|+..|..++||+...++.||..|+|++.+|+|||||||+|+|+........
T Consensus 3 ~~~~~rr~Rt~ft---~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~~ 72 (80)
T 2dms_A 3 SGSSGRRERTTFT---RAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNG 72 (80)
T ss_dssp CCCCCCCCCSSCC---HHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCCCC
T ss_pred CCCCCCCCCCCCC---HHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 9999998999899---999999999997259979999999999979398991241387757756987714789
No 6
>2dmq_A LIM/homeobox protein LHX9; 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=118.06 Aligned_cols=69 Identities=29% Similarity=0.519 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCC
Q ss_conf 999999897445798578999999976417999989999999993999654100033341112788871100
Q 001512 879 PGSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPSSKNAK 950 (1063)
Q Consensus 879 ~gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~~~~~~ 950 (1063)
.++..+|.|+.|+ ..|+..|+..|..++||+...+..||..|+|++.+|+|||||||+|+|+.......
T Consensus 3 ~~~~~rr~Rt~ft---~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~~~ 71 (80)
T 2dmq_A 3 SGSSGKRMRTSFK---HHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQEN 71 (80)
T ss_dssp CCCCCCCCCCCCC---HHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSSCC
T ss_pred CCCCCCCCCCCCC---HHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHHHHHHC
T ss_conf 9999998999989---99999999999983999999999999995989899637348777999998888716
No 7
>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=118.04 Aligned_cols=66 Identities=21% Similarity=0.396 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCC
Q ss_conf 999999897445798578999999976417999989999999993999654100033341112788871
Q 001512 879 PGSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPSSK 947 (1063)
Q Consensus 879 ~gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~~~ 947 (1063)
...+.+|.|+.|+ ..|+..|+..|..++||+...+..||..|||++.||+|||||||+|+|+..+.
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 VPVKKQKTRTVFS---STQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83 (84)
T ss_dssp CCSCSCCCSSCCC---HHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCCC
T ss_pred CCCCCCCCCCCCC---HHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 8889998998889---99999999999807998999999999993998999899999999988777506
No 8
>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=117.21 Aligned_cols=63 Identities=29% Similarity=0.380 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCC
Q ss_conf 999998974457985789999999764179999899999999939996541000333411127888
Q 001512 880 GSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPS 945 (1063)
Q Consensus 880 gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~ 945 (1063)
.++.||.|+.|+ ..|+..|+..|..++||+...+..||..+||+++||+|||||||+|+||.+
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 NERKRKRRTTIS---IAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 146 (146)
T ss_dssp -----CCCCCCC---HHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSCC
T ss_pred CCCCCCCCCCCC---HHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHCHHHHHHHHHHHHCCC
T ss_conf 777888876764---999999999999769989999999999969884232042176654552159
No 9
>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=116.96 Aligned_cols=65 Identities=29% Similarity=0.468 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCC
Q ss_conf 99999989744579857899999997641799998999999999399965410003334111278887
Q 001512 879 PGSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPSS 946 (1063)
Q Consensus 879 ~gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~~ 946 (1063)
...+.+|.|+.|+ ..|+..|+..|..++||+...++.||..|+|++.||+|||||||+|+|+...
T Consensus 13 ~~~~~rr~Rt~ft---~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~ 77 (80)
T 2da3_A 13 EPQRDKRLRTTIT---PEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP 77 (80)
T ss_dssp CCCCCTTCCSSCC---TTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred CCCCCCCCCCCCC---HHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf 8899998999989---9999999999982599999999999999795998968975877886713145
No 10
>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=116.63 Aligned_cols=69 Identities=23% Similarity=0.468 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCCC
Q ss_conf 999998974457985789999999764179999899999999939996541000333411127888711001
Q 001512 880 GSRGRRHRTSYRKLGEEVTQKLYNSFKENQYPNRTTKESLAKELGLTFSQVRKWFENTRWSFNHPSSKNAKL 951 (1063)
Q Consensus 880 gsk~RR~RT~ft~~~~~QL~~LEk~F~~n~YPs~~~ReeLA~kLGLterQVKVWFQNRRaK~KRq~~~~~~~ 951 (1063)
..+.++.|+.|+ ..|+..|+..|..++||+...+..||..|||++.||+|||||||+|+|+........
T Consensus 14 ~~~~rr~Rt~ft---~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~~~~ 82 (93)
T 3a01_A 14 PPKRKKPRTSFT---RIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREA 82 (93)
T ss_dssp CCCCCCCCCCCC---HHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC---
T ss_pred CCCCCCCCCCCC---HHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 988898996879---999999999997079969999999999949795435141175520335653788789
Done!