Query 046996
Match_columns 364
No_of_seqs 159 out of 941
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:34:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046996.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046996hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 6.8E-43 1.5E-47 298.8 6.9 128 24-151 1-129 (129)
2 cd00933 barnase Barnase, a mem 20.1 3.3E+02 0.0071 23.7 5.9 24 33-59 2-25 (107)
3 cd00490 Met_repressor_MetJ Met 16.7 1.2E+02 0.0026 25.7 2.4 39 31-73 50-88 (103)
4 PHA00692 hypothetical protein 16.7 55 0.0012 25.7 0.4 9 23-31 36-44 (74)
5 smart00265 BH4 BH4 Bcl-2 homol 16.4 1.5E+02 0.0033 19.7 2.4 20 33-52 4-23 (27)
6 PRK05264 transcriptional repre 15.0 1.3E+02 0.0028 25.6 2.3 39 31-73 51-89 (105)
7 COG3060 MetJ Transcriptional r 14.9 1E+02 0.0022 26.0 1.5 39 31-73 51-89 (105)
8 PF09174 Maf1: Maf1 regulator; 14.8 55 0.0012 30.1 0.0 12 56-67 137-148 (179)
9 PF01340 MetJ: Met Apo-repress 13.4 1.7E+02 0.0036 24.9 2.5 39 31-73 50-88 (104)
10 PF12672 DUF3793: Protein of u 13.1 1.3E+02 0.0029 27.6 2.0 39 27-71 83-122 (176)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=6.8e-43 Score=298.84 Aligned_cols=128 Identities=53% Similarity=1.068 Sum_probs=97.5
Q ss_pred CCCCceecCChHHHHHHHHHHHHcCCCCCc-cceeeccCCCCCCCCccccccCCceeEEEEeecCCcCCCCCCCcccccc
Q 046996 24 VMPGFRFHPTEEELVEFYLRRKVEGKRFNV-ELITFLDLYRYDPWELPALAAIGEKEWFFYVPRDRKYRNGDRPNRVTTS 102 (364)
Q Consensus 24 LPPGfRF~PTDEELV~~YLr~Ki~G~plp~-~~I~evDVY~~ePwdLP~~~~~Ge~eWYFFspr~rK~~nG~R~~R~tgg 102 (364)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+||+....++++||||+++++++.+|.|++|++++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~ 80 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGG 80 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETT
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccc
Confidence 799999999999999999999999999887 6899999999999999964444677999999999999999999999999
Q ss_pred ceEeecCCCceEecCCCceEEEEEEEEeecCCCCCCCCcCeEEEEEecC
Q 046996 103 GYWKATGADRMIKSENSRSIGLKKTLVFYSGKAPKGIRTSWIMNEYRLP 151 (364)
Q Consensus 103 G~WK~tG~~k~I~~~~G~vVG~KKtL~Fy~Gk~pkg~kTgWvMhEY~L~ 151 (364)
|+||.+|+.+.|.+.+|.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999877899999999999998888889999999999983
No 2
>cd00933 barnase Barnase, a member of the family of homologous microbial ribonucleases, catalyses the cleavage of single-stranded RNA via a two-step mechanism thought to be similar to that of pancreatic ribonuclease. The mechanism involves a transesterification to give a 2', 3'-cyclic phosphate intermediate, followed by hydrolysis to yield a 3' nucleotide. The active site residues His and Glu act as general acid-base groups during catalysis, while the Arg and Lys residues are important in binding the reactive phosphate, the latter probably binding the phosphate in the transition state. Barstar, a small 89 residue intracellular protein is a natural inhibitor of Barnase.
Probab=20.08 E-value=3.3e+02 Score=23.65 Aligned_cols=24 Identities=25% Similarity=0.094 Sum_probs=15.7
Q ss_pred ChHHHHHHHHHHHHcCCCCCccceeec
Q 046996 33 TEEELVEFYLRRKVEGKRFNVELITFL 59 (364)
Q Consensus 33 TDEELV~~YLr~Ki~G~plp~~~I~ev 59 (364)
|+.|-|..||.. .+ .||..+|.-.
T Consensus 2 ~~~~~V~~y~~~--~~-~LP~~yiTK~ 25 (107)
T cd00933 2 NTFQGVADYLQT--YH-RLPDNYITKS 25 (107)
T ss_pred chHHHHHHHHHH--hC-cCCcceEeHH
Confidence 455666778887 33 3788777543
No 3
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=16.74 E-value=1.2e+02 Score=25.70 Aligned_cols=39 Identities=26% Similarity=0.293 Sum_probs=31.9
Q ss_pred cCChHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCCccccc
Q 046996 31 HPTEEELVEFYLRRKVEGKRFNVELITFLDLYRYDPWELPALA 73 (364)
Q Consensus 31 ~PTDEELV~~YLr~Ki~G~plp~~~I~evDVY~~ePwdLP~~~ 73 (364)
|-|..||++.-..--..|+|||.+ .|+-+..|..+|...
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D----~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDD----ADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCcccccHHH
Confidence 467789998877788899999874 688889999998654
No 4
>PHA00692 hypothetical protein
Probab=16.68 E-value=55 Score=25.72 Aligned_cols=9 Identities=56% Similarity=0.966 Sum_probs=7.3
Q ss_pred CCCCCceec
Q 046996 23 VVMPGFRFH 31 (364)
Q Consensus 23 ~LPPGfRF~ 31 (364)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 469999994
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=16.41 E-value=1.5e+02 Score=19.71 Aligned_cols=20 Identities=25% Similarity=0.393 Sum_probs=15.8
Q ss_pred ChHHHHHHHHHHHHcCCCCC
Q 046996 33 TEEELVEFYLRRKVEGKRFN 52 (364)
Q Consensus 33 TDEELV~~YLr~Ki~G~plp 52 (364)
+-.|||.+|+.-|+.-+-.+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999765444
No 6
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=15.05 E-value=1.3e+02 Score=25.61 Aligned_cols=39 Identities=26% Similarity=0.279 Sum_probs=31.7
Q ss_pred cCChHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCCccccc
Q 046996 31 HPTEEELVEFYLRRKVEGKRFNVELITFLDLYRYDPWELPALA 73 (364)
Q Consensus 31 ~PTDEELV~~YLr~Ki~G~plp~~~I~evDVY~~ePwdLP~~~ 73 (364)
|-|-.||++.-..--..|+|||.+ -|+-+..|..+|+..
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~D----~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPDD----EDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCCh----hhhhhcCcccchHHH
Confidence 467789998877788899999874 688889999998644
No 7
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=14.87 E-value=1e+02 Score=25.97 Aligned_cols=39 Identities=26% Similarity=0.256 Sum_probs=31.7
Q ss_pred cCChHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCCccccc
Q 046996 31 HPTEEELVEFYLRRKVEGKRFNVELITFLDLYRYDPWELPALA 73 (364)
Q Consensus 31 ~PTDEELV~~YLr~Ki~G~plp~~~I~evDVY~~ePwdLP~~~ 73 (364)
|-|..||++.-...-..|+|+|. +.|+...-|.++|+.+
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHH
Confidence 46778888887777889999886 4788888999998754
No 8
>PF09174 Maf1: Maf1 regulator; InterPro: IPR015257 Maf1 is a negative regulator of RNA polymerase III [, ]. It targets the initiation factor TFIIIB []. ; PDB: 3NR5_A.
Probab=14.85 E-value=55 Score=30.15 Aligned_cols=12 Identities=33% Similarity=0.678 Sum_probs=6.7
Q ss_pred eeeccCCCCCCC
Q 046996 56 ITFLDLYRYDPW 67 (364)
Q Consensus 56 I~evDVY~~ePw 67 (364)
+.+||||.+.|.
T Consensus 137 l~~C~iYsy~pd 148 (179)
T PF09174_consen 137 LKDCDIYSYNPD 148 (179)
T ss_dssp GGG-EEEEE---
T ss_pred ccCceEEEEccC
Confidence 567899999994
No 9
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=13.42 E-value=1.7e+02 Score=24.87 Aligned_cols=39 Identities=31% Similarity=0.361 Sum_probs=24.9
Q ss_pred cCChHHHHHHHHHHHHcCCCCCccceeeccCCCCCCCCccccc
Q 046996 31 HPTEEELVEFYLRRKVEGKRFNVELITFLDLYRYDPWELPALA 73 (364)
Q Consensus 31 ~PTDEELV~~YLr~Ki~G~plp~~~I~evDVY~~ePwdLP~~~ 73 (364)
|-|..||++.-...-..|+|||.+ .|+-...|..+|...
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~D----~dl~kd~~d~ip~~~ 88 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPTD----DDLRKDRPDEIPAEA 88 (104)
T ss_dssp S-SHHHHHHHHHHHHHH------T----TGGGSTSGSSS-HHH
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCCccchHHH
Confidence 467889998877788899999874 688889999998654
No 10
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=13.10 E-value=1.3e+02 Score=27.59 Aligned_cols=39 Identities=13% Similarity=0.215 Sum_probs=23.2
Q ss_pred CceecCChHHHHHHHHHHHHcCCCCCccceeeccCC-CCCCCCccc
Q 046996 27 GFRFHPTEEELVEFYLRRKVEGKRFNVELITFLDLY-RYDPWELPA 71 (364)
Q Consensus 27 GfRF~PTDEELV~~YLr~Ki~G~plp~~~I~evDVY-~~ePwdLP~ 71 (364)
|| .+.+-+-+...|+.|+.... |-||+-|+ +++..|.-+
T Consensus 83 GY--~~~~~~~~L~~L~~R~~~~~----FPHEIGiFLGYPleDV~G 122 (176)
T PF12672_consen 83 GY--PDSSLEDCLEHLKKRFESGE----FPHEIGIFLGYPLEDVKG 122 (176)
T ss_pred Cc--CCCCHHHHHHHHHHHhcCCC----CCchhHhccCCCHHHHHH
Confidence 66 54444444445888885544 44667666 577666544
Done!