Query 042614
Match_columns 326
No_of_seqs 166 out of 960
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 07:53:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042614.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042614hhsearch_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 1.4E-39 2.9E-44 274.9 5.3 122 1-123 7-129 (129)
2 cd00933 barnase Barnase, a mem 19.0 4.5E+02 0.0098 22.3 6.4 61 4-78 2-70 (107)
3 smart00265 BH4 BH4 Bcl-2 homol 15.1 1.8E+02 0.0038 18.9 2.4 19 4-22 4-22 (27)
4 cd00490 Met_repressor_MetJ Met 14.4 1.3E+02 0.0029 24.8 2.1 39 2-44 50-88 (103)
5 COG3060 MetJ Transcriptional r 13.9 97 0.0021 25.5 1.2 39 2-44 51-89 (105)
6 smart00707 RPEL Repeat in Dros 13.8 1.2E+02 0.0026 19.4 1.4 10 1-10 9-18 (26)
7 PRK05264 transcriptional repre 12.9 1.5E+02 0.0032 24.8 1.9 39 2-44 51-89 (105)
8 PF07960 CBP4: CBP4; InterPro 12.6 1.1E+02 0.0023 26.8 1.1 11 2-12 30-40 (128)
9 PF13822 ACC_epsilon: Acyl-CoA 11.3 1.2E+02 0.0027 22.8 1.0 9 2-10 10-18 (62)
10 PF04700 Baculo_gp41: Structur 10.7 2.4E+02 0.0051 26.2 2.7 20 4-23 6-27 (186)
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=1.4e-39 Score=274.91 Aligned_cols=122 Identities=57% Similarity=1.159 Sum_probs=93.9
Q ss_pred CCCChHHHHHHHHHHhHcCCCCCC-cceeeccCCCCCCCCCCccccCCCceEEEEeccCCcCCCCCCCcccCCCCeEEee
Q 042614 1 FHPSDEELIVHYLTNKVASIPLPA-SIIAEIDLYKYNPWDLPRKALFGEEEWYFFTPRDRKYPNGARPNRAAASGFWKAT 79 (326)
Q Consensus 1 F~PTDEELV~~YL~~Ki~G~plp~-~~I~evDVY~~ePwdLP~~~~~g~~eWYFFspr~rKy~~G~R~nRatg~GyWKat 79 (326)
|+|||+|||.+||++|+.|.+++. .+|+++|||+++||+||+....++.+||||+++++++.+|.|++|++++|+||++
T Consensus 7 F~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~ 86 (129)
T PF02365_consen 7 FRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKST 86 (129)
T ss_dssp E---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETTEEEEEE
T ss_pred ecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccceEEeec
Confidence 899999999999999999999888 7999999999999999954444678999999999999999999999999999999
Q ss_pred cCCcceEeCCCCeEEEEEEEeeeecCCCCCCCccCeEEEEEEcC
Q 042614 80 GTDKPILTSFGTKSIGVKKALVFYEGRPPKGYKTDWIMHEYRLP 123 (326)
Q Consensus 80 G~~k~I~~~~gg~vIG~KktLvFY~gr~pkg~kT~WvMhEYrL~ 123 (326)
|++++|.+. ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 87 g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 87 GKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp CEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999986 7899999999999999888999999999999984
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=18.96 E-value=4.5e+02 Score=22.29 Aligned_cols=61 Identities=25% Similarity=0.559 Sum_probs=33.3
Q ss_pred ChHHHHHHHHHHhHcCCCCCCcceee--ccCCCCCC-----CCC-CccccCCCceEEEEeccCCcCCCCCCCcccCCCCe
Q 042614 4 SDEELIVHYLTNKVASIPLPASIIAE--IDLYKYNP-----WDL-PRKALFGEEEWYFFTPRDRKYPNGARPNRAAASGF 75 (326)
Q Consensus 4 TDEELV~~YL~~Ki~G~plp~~~I~e--vDVY~~eP-----wdL-P~~~~~g~~eWYFFspr~rKy~~G~R~nRatg~Gy 75 (326)
|+.|=|..||.. .+ .||..+|.- +-=-+..| |+. |+++..|+- |..+++.-|. ..+|+
T Consensus 2 ~~~~~V~~y~~~--~~-~LP~~yiTK~ea~~lGW~~~~~~L~~~~pgk~igGd~----F~N~E~~LP~-------~~~~~ 67 (107)
T cd00933 2 NTFQGVADYLQT--YH-RLPDNYITKSQAKELGWVAPKGNLWDVAPGKSIGGDR----FSNREGRLPA-------AGGRT 67 (107)
T ss_pred chHHHHHHHHHH--hC-cCCcceEeHHHHHHhccCCCCCCHhHcCCCcccCCCe----EccCCCcCCC-------CCCCe
Confidence 445556679987 34 488888864 33333443 332 555443333 6655554443 24678
Q ss_pred EEe
Q 042614 76 WKA 78 (326)
Q Consensus 76 WKa 78 (326)
|+-
T Consensus 68 y~E 70 (107)
T cd00933 68 WRE 70 (107)
T ss_pred EEE
Confidence 854
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=15.13 E-value=1.8e+02 Score=18.88 Aligned_cols=19 Identities=32% Similarity=0.530 Sum_probs=14.9
Q ss_pred ChHHHHHHHHHHhHcCCCC
Q 042614 4 SDEELIVHYLTNKVASIPL 22 (326)
Q Consensus 4 TDEELV~~YL~~Ki~G~pl 22 (326)
+-.|||.+|+.-|+.-+-.
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999965543
No 4
>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=14.44 E-value=1.3e+02 Score=24.83 Aligned_cols=39 Identities=28% Similarity=0.503 Sum_probs=31.1
Q ss_pred CCChHHHHHHHHHHhHcCCCCCCcceeeccCCCCCCCCCCccc
Q 042614 2 HPSDEELIVHYLTNKVASIPLPASIIAEIDLYKYNPWDLPRKA 44 (326)
Q Consensus 2 ~PTDEELV~~YL~~Ki~G~plp~~~I~evDVY~~ePwdLP~~~ 44 (326)
|-|-.||+..-...-..|+|||. +.|+-+..|.++|..+
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHHH
Confidence 45677888776677889999997 4689999999999754
No 5
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=13.86 E-value=97 Score=25.47 Aligned_cols=39 Identities=28% Similarity=0.510 Sum_probs=31.1
Q ss_pred CCChHHHHHHHHHHhHcCCCCCCcceeeccCCCCCCCCCCccc
Q 042614 2 HPSDEELIVHYLTNKVASIPLPASIIAEIDLYKYNPWDLPRKA 44 (326)
Q Consensus 2 ~PTDEELV~~YL~~Ki~G~plp~~~I~evDVY~~ePwdLP~~~ 44 (326)
|-|..||+..-...-..|+|+|. +.|+-+.-|.++|..+
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHH
Confidence 45667887776667889999986 5799999999999764
No 6
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=13.79 E-value=1.2e+02 Score=19.42 Aligned_cols=10 Identities=40% Similarity=0.448 Sum_probs=8.5
Q ss_pred CCCChHHHHH
Q 042614 1 FHPSDEELIV 10 (326)
Q Consensus 1 F~PTDEELV~ 10 (326)
++|+.||||.
T Consensus 9 ~RP~~eeLv~ 18 (26)
T smart00707 9 QRPTREELEE 18 (26)
T ss_pred cCCCHHHHHH
Confidence 4899999986
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=12.86 E-value=1.5e+02 Score=24.77 Aligned_cols=39 Identities=28% Similarity=0.486 Sum_probs=31.0
Q ss_pred CCChHHHHHHHHHHhHcCCCCCCcceeeccCCCCCCCCCCccc
Q 042614 2 HPSDEELIVHYLTNKVASIPLPASIIAEIDLYKYNPWDLPRKA 44 (326)
Q Consensus 2 ~PTDEELV~~YL~~Ki~G~plp~~~I~evDVY~~ePwdLP~~~ 44 (326)
|-|-.||+..-...-..|+|||. +-|+-+..|.++|..+
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHHH
Confidence 45677888776667889999997 4689999999999654
No 8
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=12.65 E-value=1.1e+02 Score=26.80 Aligned_cols=11 Identities=45% Similarity=0.921 Sum_probs=9.2
Q ss_pred CCChHHHHHHH
Q 042614 2 HPSDEELIVHY 12 (326)
Q Consensus 2 ~PTDEELV~~Y 12 (326)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 59999999765
No 9
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=11.32 E-value=1.2e+02 Score=22.77 Aligned_cols=9 Identities=56% Similarity=0.944 Sum_probs=7.2
Q ss_pred CCChHHHHH
Q 042614 2 HPSDEELIV 10 (326)
Q Consensus 2 ~PTDEELV~ 10 (326)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 699999854
No 10
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=10.66 E-value=2.4e+02 Score=26.20 Aligned_cols=20 Identities=45% Similarity=0.597 Sum_probs=12.9
Q ss_pred ChHHHHHHHHH--HhHcCCCCC
Q 042614 4 SDEELIVHYLT--NKVASIPLP 23 (326)
Q Consensus 4 TDEELV~~YL~--~Ki~G~plp 23 (326)
+|||||.||-+ +|..|...+
T Consensus 6 sDe~Li~yY~~L~K~~g~~~~~ 27 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGSDVP 27 (186)
T ss_pred cHHHHHHHHHHHHHHhCCCCCC
Confidence 68888888844 455554443
Done!