Query 005563
Match_columns 691
No_of_seqs 253 out of 548
Neff 3.5
Searched_HMMs 29240
Date Tue Mar 26 22:10:19 2013
Command hhsearch -i /local_scratch/syshi/lefta3m2/005563.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H2_126-130//hhsearch_pdb/005563hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1wid_A DNA-binding protein RAV 1.0 1 1 199.7 12.6 120 131-253 3-127 (130)
2 2l7p_A Histone-lysine N-methyl 1.0 1 1 144.9 3.7 62 370-432 22-87 (100)
3 2e61_A Zinc finger CW-type PWW 1.0 1 1 127.0 3.2 52 369-421 11-67 (69)
4 4i1k_A B3 domain-containing tr 1.0 1 1 121.4 10.6 99 137-243 44-143 (146)
5 1yel_A AT1G16640; CESG, protei 1.0 1 1 100.3 10.0 95 138-242 7-101 (104)
6 4gut_A Lysine-specific histone 1.0 1 1 50.6 -1.1 14 41-54 136-149 (776)
7 1na6_A Ecorii, restriction end 1.0 1 1 34.9 5.4 91 138-229 17-123 (404)
8 3kv5_D JMJC domain-containing 1.0 1 1 30.2 -0.2 23 409-431 370-392 (488)
9 2ri7_A Nucleosome-remodeling f 1.0 1 1 27.3 -0.1 33 372-404 19-57 (174)
10 3kqi_A GRC5, PHD finger protei 1.0 1 1 26.3 1.5 31 372-402 21-57 (75)
No 1
>1wid_A DNA-binding protein RAV1; DNA-binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: b.142.1.2
Probab=1.00 E-value=1 Score=199.69 Aligned_cols=120 Identities=38% Similarity=0.717 Sum_probs=104.9
Q ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCEEEEHHCCCCCCCCCCC---CCCCEEEEEECCCCEEEEEEEEECCCCCCCCCC-
Q ss_conf 1899874133089844425689999477300002014999999---999229999599993999999908999756001-
Q 005563 131 SGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQ---PEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVL- 206 (691)
Q Consensus 131 s~~~~~~~~~LFeKvLT~SDVgklgRLVIPK~~AE~~FPpL~~---~~Gi~L~V~D~~GK~W~FRfsyw~nn~SR~YVL- 206 (691)
++..+.+..++|+|+||+|||++++||+||+++|+.|||+++. ..++.|.++|..|++|+|+|+|| +.+++|+|
T Consensus 3 ~~~~~~~~~~~F~K~Lt~SDv~~~~rL~iPk~~a~~~lP~~~~~~~~~~~~l~l~D~~Gk~W~fr~~~~--~~~~~~~Lt 80 (130)
T 1wid_A 3 SGSSGRSAEALFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYW--NSSQSYVLT 80 (130)
T ss_dssp -----CCCEEEEEEECCTTTTSSSCCEEECHHHHTTTSCCCSSCCSSCCEEEEEEETTTEEEEEEEEEE--TTTTEEEEE
T ss_pred CCCCCCCCCCEEEEEEEHHHCCCCCEEEECHHHHHHHCCCCCCCCCCCCEEEEEEECCCCEEEEEEEEE--CCCCCEEEC
T ss_conf 877899986249999855771897779967899996688654445788389999958999999999997--899963883
Q ss_pred CCCHHHHHCCCCCCCCEEEEEEECC-CCEEEEEEEECCCCCCCCCCCC
Q ss_conf 3821253116888898899997459-9819999996689888763322
Q 005563 207 EGVTPCIQNMQLQAGDIVTFSRLEP-EGKLVMGFRKASSASASDQDNE 253 (691)
Q Consensus 207 tGWs~FVKsK~LkaGDtVvF~R~e~-~GkL~IGVRRa~~~~~s~q~~~ 253 (691)
.||..||++|+|++||+|+|++.+. +++|+|++||+.... ++|.++
T Consensus 81 ~GW~~FV~~~~L~~GD~~~F~~~~~~~~~l~I~~rr~~~~~-~~~~~~ 127 (130)
T 1wid_A 81 KGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSD-LDASGP 127 (130)
T ss_dssp SSHHHHHHHTTCCTTCEEEEEECCSSSCCEEEEEECCCSCS-SCC---
T ss_pred CCHHHHHHHCCCCCCCEEEEEEECCCCCEEEEEEEECCCCC-CCCCCC
T ss_conf 77488778719988989999995389968999999899998-665688
No 2
>2l7p_A Histone-lysine N-methyltransferase ASHH2; CW-domain; NMR {Arabidopsis thaliana}
Probab=1.00 E-value=1 Score=144.93 Aligned_cols=62 Identities=32% Similarity=0.776 Sum_probs=56.2
Q ss_pred CCCCCCEEECCCCCCCCCCCCCC----CCCCCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf 78878648306662111458999----8999917624898999998894423774888877299992
Q 005563 370 VGEKIQWVQCEDCSKWRKVPANA----RLPSKWTCSGNLWDPERSVCSVAQELREEQLEDLIAPNNP 432 (691)
Q Consensus 370 ~ge~~~WVQCD~C~KWRkLP~~~----~lP~~W~CsmN~WDp~~~sCsaPEE~~deel~~Ll~~~~~ 432 (691)
.....+|||||+|+|||+||..+ .+|++|||+||+ |+.+++|++|||.++++|+.+|++...
T Consensus 22 ~~~~~~WVQCD~C~KWRrLP~~~~~~~~~pd~W~C~mN~-D~~~nsCs~PEE~~~~ei~~~l~~~~~ 87 (100)
T 2l7p_A 22 YSTESAWVRCDDCFKWRRIPASVVGSIDESSRWICMNNS-DKRFADCSKSQEMSNEEINEELGIGQD 87 (100)
T ss_dssp CSSSSEEEECTTTCCEEEECHHHHTTSTTSSCCCGGGSS-CSSSCSTTSCCSSCHHHHHHHHTCCCC
T ss_pred CCCCCEEEEECCCCCCCCCCHHHCCCCCCCCCCEECCCC-CCCCCCCCCCCCCCHHHHHHHHCCCCC
T ss_conf 787880784078783111886675254899876607899-987788888657898999988660523
No 3
>2e61_A Zinc finger CW-type PWWP domain protein 1; ZF-CW domain, structural genomics, NPPSFA, national project protein structural and functional analyses; NMR {Homo sapiens} PDB: 2rr4_A*
Probab=1.00 E-value=1 Score=127.03 Aligned_cols=52 Identities=35% Similarity=0.891 Sum_probs=47.2
Q ss_pred CCCCCCCEEECC--CCCCCCCCCCCC---CCCCCCEEECCCCCCCCCCCCCCCCCCHH
Q ss_conf 878878648306--662111458999---89999176248989999988944237748
Q 005563 369 NVGEKIQWVQCE--DCSKWRKVPANA---RLPSKWTCSGNLWDPERSVCSVAQELREE 421 (691)
Q Consensus 369 ~~ge~~~WVQCD--~C~KWRkLP~~~---~lP~~W~CsmN~WDp~~~sCsaPEE~~de 421 (691)
..++..+||||| +|+|||+||..+ .+|++|||+||+ |+.+++|++|||.++.
T Consensus 11 ~~~~~~~WVQCd~p~C~KWR~LP~~~~~~~lpd~W~C~mN~-d~~~~~Cs~pEE~~~~ 67 (69)
T 2e61_A 11 GFGQCLVWVQCSFPNCGKWRRLCGNIDPSVLPDNWSCDQNT-DVQYNRCDIPEETWTG 67 (69)
T ss_dssp SCCCCCCEEECSSTTTCCEEECCSSCCTTTSCTTCCGGGCS-CGGGCSSSSCCCCCCC
T ss_pred CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEECCCC-CCCCCCCCCCCCCCCC
T ss_conf 77889817876944267104883300611289757858889-9766788987566777
No 4
>4i1k_A B3 domain-containing transcription factor VRN1; B3 domain beta-barrel, DNA binding protein; 1.60A {Arabidopsis thaliana}
Probab=1.00 E-value=1 Score=121.37 Aligned_cols=99 Identities=24% Similarity=0.279 Sum_probs=83.3
Q ss_pred CCCCEEEEECCCCCCCCCCCEEEEHHCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCHHHHHCC
Q ss_conf 41330898444256899994773000020149999999992299995999939999999089997560013821253116
Q 005563 137 VITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNM 216 (691)
Q Consensus 137 ~~~~LFeKvLT~SDVgklgRLVIPK~~AE~~FPpL~~~~Gi~L~V~D~~GK~W~FRfsyw~nn~SR~YVLtGWs~FVKsK 216 (691)
.-.+.|.|+|++|||.+..+|+||+.+++.|||.. ...+.++|. |+.|.|++.|+ + +++++..||..||+++
T Consensus 44 s~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~----~~~i~L~~~-gk~W~v~~~~~--~-~~~~ls~GW~~Fv~dn 115 (146)
T 4i1k_A 44 PTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGI----SGFIKVQLA-EKQWPVRCLYK--A-GRAKFSQGWYEFTLEN 115 (146)
T ss_dssp CSSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTC----CSEEEEEET-TEEEEEEEEEE--T-TEEEECTTHHHHHHHT
T ss_pred CCCCEEEEEECCHHCCCCCEEEECHHHHHHHCCCC----CEEEEEEEC-CCEEEEEEEEE--C-CCEEECCCHHHHHHHC
T ss_conf 99998999978566189867990999999748888----837999979-94789899995--8-9078777638988875
Q ss_pred CCCCCCEEEEEEECCCC-EEEEEEEECC
Q ss_conf 88889889999745998-1999999668
Q 005563 217 QLQAGDIVTFSRLEPEG-KLVMGFRKAS 243 (691)
Q Consensus 217 ~LkaGDtVvF~R~e~~G-kL~IGVRRa~ 243 (691)
+|++||+|+|...+... .|.|.|-|+.
T Consensus 116 ~L~~GD~cvFeli~~~~~~f~V~IfR~~ 143 (146)
T 4i1k_A 116 NLGEGDVCVFELLRTRDFVLKVTAFRVN 143 (146)
T ss_dssp TCCTTCEEEEEECSSSSCEEEEEEECCC
T ss_pred CCCCCCEEEEEEECCCCEEEEEEEEECC
T ss_conf 9998989999993698659999999445
No 5
>1yel_A AT1G16640; CESG, protein structure initiative, structural genomics, center for eukaryotic structural genomics, unknown function; NMR {Arabidopsis thaliana} SCOP: b.142.1.2
Probab=1.00 E-value=1 Score=100.34 Aligned_cols=95 Identities=14% Similarity=0.266 Sum_probs=77.0
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEHHCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCHHHHHCCC
Q ss_conf 13308984442568999947730000201499999999922999959999399999990899975600138212531168
Q 005563 138 ITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQ 217 (691)
Q Consensus 138 ~~~LFeKvLT~SDVgklgRLVIPK~~AE~~FPpL~~~~Gi~L~V~D~~GK~W~FRfsyw~nn~SR~YVLtGWs~FVKsK~ 217 (691)
..+.|.|+|+++|.. .+|.||++.++.+.+.+ +..+.++|..|+.|.++++++. .+.++..||..||++++
T Consensus 7 ~~p~F~K~l~~~~~~--~~L~IP~~F~~~~~~~~----~~~v~L~~~~G~~W~v~~~~~~---~~~~l~~GW~~Fv~~~~ 77 (104)
T 1yel_A 7 GEVQFMKPFISEKSS--KSLEIPLGFNEYFPAPF----PITVDLLDYSGRSWTVRMKKRG---EKVFLTVGWENFVKDNN 77 (104)
T ss_dssp CCEEEEEECCHHHHT--TCEECCHHHHTTCCCCC----CSEEEEEETTSCEEEEEEEEET---TEEEECTTHHHHHHHHT
T ss_pred CCCCEEEEECCCCCC--CEEECCHHHHHHCCCCC----CCEEEEECCCCCEEEEEEEEEC---CCEEECCCHHHHHHHCC
T ss_conf 898789998777755--31888999998648669----9889999799999999999989---94998629499999759
Q ss_pred CCCCCEEEEEEECCCCEEEEEEEEC
Q ss_conf 8889889999745998199999966
Q 005563 218 LQAGDIVTFSRLEPEGKLVMGFRKA 242 (691)
Q Consensus 218 LkaGDtVvF~R~e~~GkL~IGVRRa 242 (691)
|++||.|+|.... +..+.|-|=+.
T Consensus 78 L~~GD~lvF~~~~-~~~f~V~If~~ 101 (104)
T 1yel_A 78 LEDGKYLQFIYDR-DRTFYVIIYGH 101 (104)
T ss_dssp CCTTCEEEEEECS-SSEEEEEEECS
T ss_pred CCCCCEEEEEECC-CCEEEEEEECC
T ss_conf 9989899999858-97699999789
No 6
>4gut_A Lysine-specific histone demethylase 1B; histone demethylase; HET: FAD PGE; 2.00A {Homo sapiens} PDB: 4gur_A* 4gus_A* 4guu_A* 4fwe_A* 4fwf_A* 4fwj_A* 4gu1_A*
Probab=1.00 E-value=1 Score=50.64 Aligned_cols=14 Identities=21% Similarity=0.036 Sum_probs=5.6
Q ss_pred CCCCCCCCCCCCCC
Q ss_conf 79999975431135
Q 005563 41 DDSSTPHFGLAVSY 54 (691)
Q Consensus 41 ~~~~~~~~~~~~~~ 54 (691)
-|+|..|-..-|-.
T Consensus 136 ~~~~~~~~~~~~~~ 149 (776)
T 4gut_A 136 SDHCSLPEDLRVLE 149 (776)
T ss_dssp CCGGGSCCCHHHHH
T ss_pred CCCCCCCCCCCHHH
T ss_conf 88778974200201
No 7
>1na6_A Ecorii, restriction endonuclease ecorii; site-specific restriction, mutation, replication, hydrolase; 2.10A {Escherichia coli} SCOP: b.142.1.1 c.52.1.22 PDB: 3hqg_A 3hqf_A
Probab=1.00 E-value=1 Score=34.94 Aligned_cols=91 Identities=16% Similarity=0.159 Sum_probs=62.4
Q ss_pred CCCEEEEECCCCCCCC----CCCEEEEHHCCCCCCCCCCCC---C-CCEEEE--EECCCCEEEEEEEEECC-----CCCC
Q ss_conf 1330898444256899----994773000020149999999---9-922999--95999939999999089-----9975
Q 005563 138 ITPLFEKMLSASDAGR----IGRLVLPKKCAEAYFPPISQP---E-GLPLKV--QDSKGKEWIFQFRFWPN-----NNSR 202 (691)
Q Consensus 138 ~~~LFeKvLT~SDVgk----lgRLVIPK~~AE~~FPpL~~~---~-Gi~L~V--~D~~GK~W~FRfsyw~n-----n~SR 202 (691)
....|.|.|++.|++. ...+.+|+...+.+||.++.. . ...+.+ -|...-.+.++++|+ | ..+.
T Consensus 17 ~~~v~~K~LSAnDtgatgshQ~gi~ipk~~l~~lfp~lg~~~e~~~~~~~~~~l~d~d~p~td~~~twY-n~R~~~~tRn 95 (404)
T 1na6_A 17 NYFVYIKRLSANDTGATGGHQVGLYIPSGIVEKLFPSINHTRELNPSVFLTAHVSSHDCPDSEARAIYY-NSAHFGKTRN 95 (404)
T ss_dssp SEEEEEEECCHHHHTCC---CCCCCCCHHHHHHHCGGGCCCSSSSCEEEEEEEESSSCCCCEEEEEEEE-CGGGTTSCCC
T ss_pred CCHHEEEECCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCEEEEEEEEE-CCCCCCCCCC
T ss_conf 604135772244578877764445785689998635489865567763157784168884277899983-2646689887
Q ss_pred CCCCCCCH-HHHHCCCCCCCCEEEEEEE
Q ss_conf 60013821-2531168888988999974
Q 005563 203 MYVLEGVT-PCIQNMQLQAGDIVTFSRL 229 (691)
Q Consensus 203 ~YVLtGWs-~FVKsK~LkaGDtVvF~R~ 229 (691)
.|-|+.|. .+.=.....+||.++|.+.
T Consensus 96 EyRLt~~~~~~~~~~~a~~GDLlvia~~ 123 (404)
T 1na6_A 96 EKRITRWGRGSPLQDPENTGALTLLAFK 123 (404)
T ss_dssp EEEEECCCTTSGGGCGGGTTCEEEEEEE
T ss_pred CEEEEECCCCCCCCCCCCCCCEEEEEEE
T ss_conf 4588402789865466888788999872
No 8
>3kv5_D JMJC domain-containing histone demethylation protein 1D; epigenetics, histone CODE, jumonji lysine demethylase, metal-binding, zinc, zinc-finger; HET: OGA; 2.39A {Homo sapiens} PDB: 3kv6_A*
Probab=1.00 E-value=1 Score=30.19 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=16.1
Q ss_pred CCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf 99889442377488887729999
Q 005563 409 RSVCSVAQELREEQLEDLIAPNN 431 (691)
Q Consensus 409 ~~sCsaPEE~~deel~~Ll~~~~ 431 (691)
.+++.++.++.--+++..+....
T Consensus 370 ~~~~nl~~~l~~~~~e~~~~~~~ 392 (488)
T 3kv5_D 370 LHNLNIGMQLRCYEMEKRLKTPD 392 (488)
T ss_dssp CCSTTHHHHHHHHHHHHHTTCCT
T ss_pred CCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 77567999999999998508863
No 9
>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*
Probab=1.00 E-value=1 Score=27.25 Aligned_cols=33 Identities=21% Similarity=0.547 Sum_probs=21.8
Q ss_pred CCCCEEECCCCCCCCCCC---CC---CCCCCCCEEECCC
Q ss_conf 878648306662111458---99---9899991762489
Q 005563 372 EKIQWVQCEDCSKWRKVP---AN---ARLPSKWTCSGNL 404 (691)
Q Consensus 372 e~~~WVQCD~C~KWRkLP---~~---~~lP~~W~CsmN~ 404 (691)
+...|||||.|..|=-.. .. ...++.|+|..-.
T Consensus 19 ~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~ 57 (174)
T 2ri7_A 19 ESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQ 57 (174)
T ss_dssp TTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHH
T ss_pred CCCCEEECCCCCCHHCHHHCCCCHHHCCCCCCEECCCCC
T ss_conf 999886789998020863269751122576675648994
No 10
>3kqi_A GRC5, PHD finger protein 2; metal-binding, zinc-finger, histone-binding, NUC protein; HET: M3L; 1.78A {Homo sapiens} SCOP: g.50.1.2
Probab=1.00 E-value=1 Score=26.31 Aligned_cols=31 Identities=16% Similarity=0.443 Sum_probs=20.3
Q ss_pred CCCCEEECCCCCCCCCC------CCCCCCCCCCEEEC
Q ss_conf 87864830666211145------89998999917624
Q 005563 372 EKIQWVQCEDCSKWRKV------PANARLPSKWTCSG 402 (691)
Q Consensus 372 e~~~WVQCD~C~KWRkL------P~~~~lP~~W~Csm 402 (691)
....|||||.|..|=-. ...+...+.|+|..
T Consensus 21 ~~~~MI~Cd~C~~WfH~~Cvg~~~~~~~~~~~~~C~~ 57 (75)
T 3kqi_A 21 VTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPN 57 (75)
T ss_dssp TTSCEEECTTTCCEEEHHHHTCCTTTGGGBSSCCCHH
T ss_pred CCCCEEECCCCCCCEECCCCCCCCCCCCCCCEEECCC
T ss_conf 9977787379998773340662634447899899998
Done!