Query 002739
Match_columns 886
No_of_seqs 241 out of 507
Neff 3.5
Searched_HMMs 29240
Date Tue Mar 26 21:54:10 2013
Command hhsearch -i /local_scratch/syshi/lefta3m2/002739.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H2_104-107//hhsearch_pdb/002739hhsearch_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 13.0 120 326-448 3-127 (130)
2 2l7p_A Histone-lysine N-methyl 1.0 1 1 144.9 2.8 62 565-627 22-87 (100)
3 2e61_A Zinc finger CW-type PWW 1.0 1 1 127.4 3.0 53 564-617 11-68 (69)
4 4i1k_A B3 domain-containing tr 1.0 1 1 120.8 11.8 98 333-438 45-143 (146)
5 1yel_A AT1G16640; CESG, protei 1.0 1 1 99.5 10.9 95 333-437 7-101 (104)
6 4gut_A Lysine-specific histone 1.0 1 1 47.8 -0.9 81 4-85 3-138 (776)
7 4gat_A Nitrogen regulatory pro 1.0 1 1 35.1 1.2 37 2-45 6-42 (66)
8 3dfx_A Trans-acting T-cell-spe 1.0 1 1 33.4 2.1 37 4-47 6-42 (63)
9 1gnf_A Transcription factor GA 1.0 1 1 33.3 2.1 36 3-45 2-37 (46)
10 2kae_A GATA-type transcription 1.0 1 1 32.8 1.8 36 4-45 7-42 (71)
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=199.75 Aligned_cols=120 Identities=38% Similarity=0.717 Sum_probs=105.3
Q ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCEEEEHHHHHHCCCCCCC---CCCCEEEEEECCCCEEEEEEEECCCCCCCCCCCC
Q ss_conf 2899862011099845504479999598302335310999999---9993399996999939999999299998550123
Q 002739 326 SGDSNSVITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQ---PEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLE 402 (886)
Q Consensus 326 sg~~ns~~~~LF~KvLT~SDVgslgRLVIPKk~AEa~FPpL~~---~egi~L~V~D~~GK~W~FRfsyw~NN~SR~YVLt 402 (886)
+|.++....++|+|+||+|||++.+||+||+++|+.|||.++. .+++.|.++|.+|++|+|+|+|| +.+++|+|+
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 -CCHHHHHCCCCCCCCEEEEEEEC-CCCEEEEEEEECCCCCCCCHHHH
Q ss_conf -82236420588789889999745-99829999995799767520110
Q 002739 403 -GVTPCIQNMQLQAGDIVTFSRLE-PEGKLVMGFRKASSASASDQDNE 448 (886)
Q Consensus 403 -GW~~FVRsK~LkaGDtVvF~R~e-~~GkL~IGVRRa~~~~~s~q~~~ 448 (886)
||..||++|+|++||+|+|++.+ .+++|+|++||+.... ++|.+.
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=56.0
Q ss_pred CCCCCCEEECCCCCCCCCCCCCC----CCCCCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHCCCCC
Q ss_conf 78868559536762001568998----8999937624898999998881101543667766299991
Q 002739 565 VGEKIQWVQCEDCSKWRKVPANA----RLPSKWTCSGNLWDPERSVCSVAQELREEQLEDLIAPNNP 627 (886)
Q Consensus 565 ~ge~~~WVQCD~C~KWRkLP~~~----~lP~kW~CsmN~WDp~~~sCsaPEE~~~~el~~lL~~~~~ 627 (886)
.....+|||||.|+|||+||..+ .+|++|||+||+ |+.|++|++|||.++++|+.+|+++..
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=127.45 Aligned_cols=53 Identities=34% Similarity=0.864 Sum_probs=47.8
Q ss_pred CCCCCCCEEECC--CCCCCCCCCCCC---CCCCCCEEECCCCCCCCCCCCCCCCCCHHH
Q ss_conf 878868559536--762001568998---899993762489899999888110154366
Q 002739 564 NVGEKIQWVQCE--DCSKWRKVPANA---RLPSKWTCSGNLWDPERSVCSVAQELREEQ 617 (886)
Q Consensus 564 ~~ge~~~WVQCD--~C~KWRkLP~~~---~lP~kW~CsmN~WDp~~~sCsaPEE~~~~e 617 (886)
..++..+||||| .|+|||+||..+ .+|++|||+||+ |+.+++|++|||.++..
T Consensus 11 ~~~~~~~WVQCd~p~C~KWR~LP~~~~~~~lpd~W~C~mN~-d~~~~~Cs~pEE~~~~~ 68 (69)
T 2e61_A 11 GFGQCLVWVQCSFPNCGKWRRLCGNIDPSVLPDNWSCDQNT-DVQYNRCDIPEETWTGL 68 (69)
T ss_dssp SCCCCCCEEECSSTTTCCEEECCSSCCTTTSCTTCCGGGCS-CGGGCSSSSCCCCCCCC
T ss_pred CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEECCCC-CCCCCCCCCCCCCCCCC
T ss_conf 77889817876944267104883300611289757858889-97667889875667777
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=120.76 Aligned_cols=98 Identities=24% Similarity=0.288 Sum_probs=82.5
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCCCCCCCCCCCHHHHHCCC
Q ss_conf 01109984550447999959830233531099999999933999969999399999992999985501238223642058
Q 002739 333 ITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQ 412 (886)
Q Consensus 333 ~~~LF~KvLT~SDVgslgRLVIPKk~AEa~FPpL~~~egi~L~V~D~~GK~W~FRfsyw~NN~SR~YVLtGW~~FVRsK~ 412 (886)
-.+.|+|+|++|||.+..+|.||+..++.|||.. ...+.++|. |+.|.|++.|+ + +++++..||..||++++
T Consensus 45 ~~P~Fvk~l~~S~v~~~~~L~IP~~Fa~~~lp~~----~~~i~L~~~-gk~W~v~~~~~--~-~~~~ls~GW~~Fv~dn~ 116 (146)
T 4i1k_A 45 TNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGI----SGFIKVQLA-EKQWPVRCLYK--A-GRAKFSQGWYEFTLENN 116 (146)
T ss_dssp SSCEEEEECCGGGSSTTCCEECCHHHHHHHCTTC----CSEEEEEET-TEEEEEEEEEE--T-TEEEECTTHHHHHHHTT
T ss_pred CCCEEEEEECCHHCCCCCEEEECHHHHHHHCCCC----CEEEEEEEC-CCEEEEEEEEE--C-CCEEECCCHHHHHHHCC
T ss_conf 9998999978566189867990999999748888----837999979-94789899995--8-90787776389888759
Q ss_pred CCCCCEEEEEEECCCC-EEEEEEEECC
Q ss_conf 8789889999745998-2999999579
Q 002739 413 LQAGDIVTFSRLEPEG-KLVMGFRKAS 438 (886)
Q Consensus 413 LkaGDtVvF~R~e~~G-kL~IGVRRa~ 438 (886)
|++||+|+|...+... .|.|.|-|+.
T Consensus 117 L~~GD~cvFeli~~~~~~f~V~IfR~~ 143 (146)
T 4i1k_A 117 LGEGDVCVFELLRTRDFVLKVTAFRVN 143 (146)
T ss_dssp CCTTCEEEEEECSSSSCEEEEEEECCC
T ss_pred CCCCCEEEEEEECCCCEEEEEEEEECC
T ss_conf 998989999993698659999999445
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=99.52 Aligned_cols=95 Identities=14% Similarity=0.272 Sum_probs=77.6
Q ss_pred CCCEEEEECCCCCCCCCCCEEEEHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCCCCCCCCCCCHHHHHCCC
Q ss_conf 01109984550447999959830233531099999999933999969999399999992999985501238223642058
Q 002739 333 ITPLFEKMLSASDAGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDSKGKEWIFQFRFWPNNNSRMYVLEGVTPCIQNMQ 412 (886)
Q Consensus 333 ~~~LF~KvLT~SDVgslgRLVIPKk~AEa~FPpL~~~egi~L~V~D~~GK~W~FRfsyw~NN~SR~YVLtGW~~FVRsK~ 412 (886)
..+.|.|+|+++|.. .+|.||++.++.+.+.+ ...+.++|..|+.|.+++.++ ..+.++..||..||++++
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----PITVDLLDYSGRSWTVRMKKR---GEKVFLTVGWENFVKDNN 77 (104)
T ss_dssp CCEEEEEECCHHHHT--TCEECCHHHHTTCCCCC----CSEEEEEETTSCEEEEEEEEE---TTEEEECTTHHHHHHHHT
T ss_pred CCCCEEEEECCCCCC--CEEECCHHHHHHCCCCC----CCEEEEECCCCCEEEEEEEEE---CCCEEECCCHHHHHHHCC
T ss_conf 898789998777755--31888999998648669----988999979999999999998---994998629499999759
Q ss_pred CCCCCEEEEEEECCCCEEEEEEEEC
Q ss_conf 8789889999745998299999957
Q 002739 413 LQAGDIVTFSRLEPEGKLVMGFRKA 437 (886)
Q Consensus 413 LkaGDtVvF~R~e~~GkL~IGVRRa 437 (886)
|++||.|+|.... +..|.|-|=+.
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=47.81 Aligned_cols=81 Identities=22% Similarity=0.421 Sum_probs=44.8
Q ss_pred CCCCCCCCCCCC-------CCCCC-----CCCCCCCCCCCHHHHHHHHHHHCCCC--CCCCCCCC---------------
Q ss_conf 675222344588-------68898-----76771035687365544554301355--22222346---------------
Q 002739 4 SSKICFNKECKE-------LKSER-----PRKGWLLRGGEFAELCDRCGSIYEEG--RFCDTFHV--------------- 54 (886)
Q Consensus 4 ~~k~C~N~~C~~-------~~s~~-----wrkGW~lRSG~~A~LCdrCgsayEq~--~FCe~FH~--------------- 54 (886)
+++.|-|+.|.+ ..+.+ -...|.--|-+= -.|.-|-..|=++ -.++.|+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~e-~~c~~c~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~ 81 (776)
T 4gut_A 3 GSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGE-HFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSP 81 (776)
T ss_dssp SBSSBSSTTCCCSSCCBSCCCSTTCCTTSCBSCEEEEETTE-EEEHHHHHHHHSTTSTTHHHHHHHHHHHHHTCCSCCCH
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEECCCC-CHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCHHH
T ss_conf 74425667875324077877888987479876136723654-01477999986147640378999999987587555669
Q ss_pred -------CCCCCCCCC--CCCC----------------CEEECCCCCCC-CCEEECC
Q ss_conf -------898831135--6899----------------01002222443-2233036
Q 002739 55 -------NASGWRCCE--SCGK----------------RVHCGCITSVH-AFTLLDA 85 (886)
Q Consensus 55 -------~~sGWR~C~--~C~K----------------rlHCGCIaS~~-~f~lLD~ 85 (886)
.-+=|-.|. .||| +--|||+...+ .++..|.
T Consensus 82 ~~~~~~~~l~~~~~c~~~~c~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~ 138 (776)
T 4gut_A 82 KAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDH 138 (776)
T ss_dssp HHHHHHHTSCCEEECCCTTTCCEEECCTTCCCCHHHHHHCCTTCCCC-------CCG
T ss_pred HHHHHHCCCCHHHHCCCCCCCCHHHCCCCCCCCHHHHHEEECCCCCCCCCCCCCCCC
T ss_conf 999873237673524853455332078767778413025665685676533466887
No 7
>4gat_A Nitrogen regulatory protein AREA; DNA binding protein, transcription factor, zinc binding domain, complex (transcription regulation/DNA); HET: DNA; NMR {Emericella nidulans} SCOP: g.39.1.1 PDB: 5gat_A* 6gat_A* 7gat_A*
Probab=1.00 E-value=1 Score=35.15 Aligned_cols=37 Identities=24% Similarity=0.516 Sum_probs=30.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 86675222344588688987677103568736554455430135
Q 002739 2 SSSSKICFNKECKELKSERPRKGWLLRGGEFAELCDRCGSIYEE 45 (886)
Q Consensus 2 ~~~~k~C~N~~C~~~~s~~wrkGW~lRSG~~A~LCdrCgsayEq 45 (886)
+...+.|.| |+++.+..||+|. .|. .||..||+-|..
T Consensus 6 ~~~~~~C~~--C~t~~Tp~WR~gp---~G~--~LCNaCGl~~~~ 42 (66)
T 4gat_A 6 QNGPTTCTN--CFTQTTPLWRRNP---EGQ--PLCNACGLFLKL 42 (66)
T ss_dssp SSSSCCCTT--TCCCCCSSCEEET---TTE--EECHHHHHHHHH
T ss_pred CCCCCCCCC--CCCCCCCCCCCCC---CCC--CCCHHHHHHHHH
T ss_conf 999899787--7998798677599---989--715777889997
No 8
>3dfx_A Trans-acting T-cell-specific transcription factor GATA-3; activator, DNA-binding, metal-binding, nucleus; HET: DNA; 2.70A {Mus musculus} PDB: 3dfv_D* 2gat_A* 3gat_A* 1gat_A* 1gau_A*
Probab=1.00 E-value=1 Score=33.45 Aligned_cols=37 Identities=24% Similarity=0.577 Sum_probs=30.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 67522234458868898767710356873655445543013552
Q 002739 4 SSKICFNKECKELKSERPRKGWLLRGGEFAELCDRCGSIYEEGR 47 (886)
Q Consensus 4 ~~k~C~N~~C~~~~s~~wrkGW~lRSG~~A~LCdrCgsayEq~~ 47 (886)
..+.|.| |+++.+..||+|.- |. .||+-||+-|....
T Consensus 6 ~~~~C~~--C~tt~Tp~WR~gp~---G~--~LCNACGl~~~~~~ 42 (63)
T 3dfx_A 6 AGTSCAN--CQTTTTTLWRRNAN---GD--PVCNACGLYYKLHN 42 (63)
T ss_dssp TTCCCTT--TCCSCCSSCCCCTT---SC--CCCHHHHHHHHHHS
T ss_pred CCCCCCC--CCCCCCCCCCCCCC---CC--CHHHHHHHHHHHCC
T ss_conf 8893887--38979984078999---98--11038899999708
No 9
>1gnf_A Transcription factor GATA-1; zinc finger, transcription regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB: 1y0j_A 2l6y_A 2l6z_A
Probab=1.00 E-value=1 Score=33.34 Aligned_cols=36 Identities=28% Similarity=0.555 Sum_probs=29.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 6675222344588688987677103568736554455430135
Q 002739 3 SSSKICFNKECKELKSERPRKGWLLRGGEFAELCDRCGSIYEE 45 (886)
Q Consensus 3 ~~~k~C~N~~C~~~~s~~wrkGW~lRSG~~A~LCdrCgsayEq 45 (886)
+..+.|.| |+++++..||+|. .|. .||+.||+-|..
T Consensus 2 ~~~~~C~~--C~tt~Tp~WR~gp---~G~--~LCNaCGl~~k~ 37 (46)
T 1gnf_A 2 SEARECVN--CGATATPLWRRDR---TGH--YLCNACGLYHKM 37 (46)
T ss_dssp CCSCCCTT--TCCCCCSSCBCCT---TCC--CBCSHHHHHHHH
T ss_pred CCCCCCCC--CCCCCCCCCCCCC---CCC--CCCHHHHHHHHH
T ss_conf 98887977--5898898574499---998--032488999998
No 10
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR {Caenorhabditis elegans}
Probab=1.00 E-value=1 Score=32.84 Aligned_cols=36 Identities=25% Similarity=0.302 Sum_probs=27.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 675222344588688987677103568736554455430135
Q 002739 4 SSKICFNKECKELKSERPRKGWLLRGGEFAELCDRCGSIYEE 45 (886)
Q Consensus 4 ~~k~C~N~~C~~~~s~~wrkGW~lRSG~~A~LCdrCgsayEq 45 (886)
..+.|.| |+++.+..||+|+.-. | .||.-||+-|..
T Consensus 7 ~~~~C~n--C~tt~Tp~WRrg~~~~-g---~LCNACGl~~~~ 42 (71)
T 2kae_A 7 KSFQCSN--CSVTETIRWRNIRSKE-G---IQCNACFIYQRK 42 (71)
T ss_dssp -CCCCSS--SCCSCCSSCCCCSSSS-C---CCSSHHHHHHHH
T ss_pred CCCCCCC--CCCCCCCCCCCCCCCC-C---CCCHHHHHHHHH
T ss_conf 8983880--3998898314589999-8---442088999998
Done!