Query 030306
Match_columns 179
No_of_seqs 108 out of 873
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 11:43:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030306.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030306hhsearch_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 7.7E-41 1.7E-45 255.4 6.8 124 2-146 3-129 (129)
2 PF07960 CBP4: CBP4; InterPro 26.7 49 0.0011 25.5 2.0 16 7-22 30-49 (128)
3 PF01473 CW_binding_1: Putativ 25.1 52 0.0011 16.4 1.3 8 71-78 7-14 (19)
4 PF13822 ACC_epsilon: Acyl-CoA 25.0 37 0.0008 22.6 0.9 19 6-24 9-30 (62)
5 cd00490 Met_repressor_MetJ Met 18.4 1.2E+02 0.0027 22.1 2.5 37 7-50 50-89 (103)
6 smart00707 RPEL Repeat in Dros 18.1 84 0.0018 17.6 1.3 12 5-16 8-19 (26)
7 PF07131 DUF1382: Protein of u 17.6 1.1E+02 0.0024 20.6 1.9 21 2-22 22-49 (61)
8 PRK05264 transcriptional repre 16.3 1.4E+02 0.003 21.9 2.4 37 7-50 51-90 (105)
9 cd01785 PDZ_GEF_RA Ubiquitin-l 16.1 64 0.0014 23.1 0.6 31 136-170 29-60 (85)
10 PF04700 Baculo_gp41: Structur 15.6 1.4E+02 0.0031 24.5 2.5 21 5-26 3-26 (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=7.7e-41 Score=255.37 Aligned_cols=124 Identities=28% Similarity=0.533 Sum_probs=91.9
Q ss_pred CCCccCCChHHHHHH-HHHhhcCCCCCCCCCceeeccC--CCCCCcCccchhhhhccccccccCCCCCCCCCCceEEEee
Q 030306 2 ETDPYNPFDQSLIKQ-LNNKIIDEPVEFPDLITTEIND--HHPADFFPGSLLRAFCTSFNNVQLPKGGDRDREKGCYVLT 78 (179)
Q Consensus 2 ~g~RF~PTDeELI~~-L~~Ki~g~pl~~~~~~I~~~Dv--~~Pw~~Lp~~~~~~~~~~~~~~~~~~g~~~~~~~~wyFFs 78 (179)
-||||+|||+|||.+ |++|+.|.+++ ..++|+++|| +|||+ |++... .++.+||||+
T Consensus 3 ~G~rF~PtD~ELi~~yL~~k~~g~~~~-~~~~i~~~Diy~~~P~~-L~~~~~------------------~~~~~~yFF~ 62 (129)
T PF02365_consen 3 PGFRFRPTDEELINHYLRPKILGEPLP-CEDVIHDVDIYSAHPWE-LPAKFK------------------GGDEEWYFFS 62 (129)
T ss_dssp TTEEE---HHHHHHCTHHHHHTT-HHC-S-CHSEE--GGGS-GGG-CHHHSS------------------S-SSEEEEEE
T ss_pred CceEecCChHHHHHHHHHHHhcCCCCC-cccceeecccCccChHH-hhhhcc------------------CCCceEEEEE
Confidence 389999999999999 99999999984 3488999999 99999 885322 4567999999
Q ss_pred ccccccCCCCCccccccceeeeecCcccceEeCCCCcEEEEEEeeeeeCCCCCCCCCcCeEEEEEEeC
Q 030306 79 PKHLLYGLTWLPERRAKNGYWKPYGYIDGRIFGACGKLVAIKQSFTFHEPGENIGRKTDWNMTEYRLL 146 (179)
Q Consensus 79 ~~~~k~~~g~R~~R~~~~G~Wk~~G~~~~~I~~~~g~~vG~kk~l~Fy~g~~~~~~kT~W~M~EY~l~ 146 (179)
++++++.++.|.+|++++|+||++| +.++|.+.+|.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 63 ~~~~~~~~~~r~~R~~~~G~Wk~~g-~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 63 PRKKKYPNGGRPNRVTGGGYWKSTG-KEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp E----------S-EEETTEEEEEEC-EEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ecccccCCcccccccccceEEeecc-cccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999999999999999 999999778999999999999998888899999999999984
No 2
>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=26.66 E-value=49 Score=25.53 Aligned_cols=16 Identities=25% Similarity=0.627 Sum_probs=12.1
Q ss_pred CCChHHHHHH----HHHhhc
Q 030306 7 NPFDQSLIKQ----LNNKII 22 (179)
Q Consensus 7 ~PTDeELI~~----L~~Ki~ 22 (179)
.||||||+.. |+++..
T Consensus 30 tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 30 TPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred CCCHHHHHHhcCHHHHHHHH
Confidence 6999999987 555444
No 3
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=25.13 E-value=52 Score=16.38 Aligned_cols=8 Identities=13% Similarity=0.330 Sum_probs=6.5
Q ss_pred CceEEEee
Q 030306 71 EKGCYVLT 78 (179)
Q Consensus 71 ~~~wyFFs 78 (179)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899995
No 4
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=24.98 E-value=37 Score=22.61 Aligned_cols=19 Identities=26% Similarity=0.303 Sum_probs=12.9
Q ss_pred cCCChHHHHHH---HHHhhcCC
Q 030306 6 YNPFDQSLIKQ---LNNKIIDE 24 (179)
Q Consensus 6 F~PTDeELI~~---L~~Ki~g~ 24 (179)
=+||||||-.. |.-.....
T Consensus 9 GnPt~eElAAL~aVlaa~~a~~ 30 (62)
T PF13822_consen 9 GNPTDEELAALTAVLAARAAAA 30 (62)
T ss_pred CCCCHHHHHHHHHHHHHHhccc
Confidence 37999999776 55444443
No 5
>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=18.37 E-value=1.2e+02 Score=22.07 Aligned_cols=37 Identities=14% Similarity=0.369 Sum_probs=29.2
Q ss_pred CCChHHHHHH-HHHhhcCCCCCCCCCceeeccC--CCCCCcCccchh
Q 030306 7 NPFDQSLIKQ-LNNKIIDEPVEFPDLITTEIND--HHPADFFPGSLL 50 (179)
Q Consensus 7 ~PTDeELI~~-L~~Ki~g~pl~~~~~~I~~~Dv--~~Pw~~Lp~~~~ 50 (179)
|-|..||++- ...-..|+|| |. +.|+ ..|.+ +|....
T Consensus 50 HATNSELLCEAFLHAfTGQPL--P~----D~Dl~K~~~d~-iP~~ak 89 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPL--PD----DADLRKERSDE-IPEAAK 89 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCC--CC----hhhhhhcCccc-ccHHHH
Confidence 4578899999 8888899999 53 5677 77777 887765
No 6
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=18.06 E-value=84 Score=17.59 Aligned_cols=12 Identities=17% Similarity=0.279 Sum_probs=10.2
Q ss_pred ccCCChHHHHHH
Q 030306 5 PYNPFDQSLIKQ 16 (179)
Q Consensus 5 RF~PTDeELI~~ 16 (179)
..+||-+|||..
T Consensus 8 ~~RP~~eeLv~r 19 (26)
T smart00707 8 SQRPTREELEER 19 (26)
T ss_pred HcCCCHHHHHHc
Confidence 478999999976
No 7
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=17.55 E-value=1.1e+02 Score=20.61 Aligned_cols=21 Identities=19% Similarity=0.218 Sum_probs=14.6
Q ss_pred CCCccCC----ChHHHHHH---HHHhhc
Q 030306 2 ETDPYNP----FDQSLIKQ---LNNKII 22 (179)
Q Consensus 2 ~g~RF~P----TDeELI~~---L~~Ki~ 22 (179)
.|.||.| ||+|+... |..|+.
T Consensus 22 ~GIRFVpiPv~~dee~~~L~s~~~~kLe 49 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHTLSSQLSQKLE 49 (61)
T ss_pred cCceeeccccccHHHHHHHHHHHHHHHH
Confidence 4789988 67777655 666653
No 8
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=16.26 E-value=1.4e+02 Score=21.94 Aligned_cols=37 Identities=14% Similarity=0.352 Sum_probs=29.0
Q ss_pred CCChHHHHHH-HHHhhcCCCCCCCCCceeeccC--CCCCCcCccchh
Q 030306 7 NPFDQSLIKQ-LNNKIIDEPVEFPDLITTEIND--HHPADFFPGSLL 50 (179)
Q Consensus 7 ~PTDeELI~~-L~~Ki~g~pl~~~~~~I~~~Dv--~~Pw~~Lp~~~~ 50 (179)
|-|..||++- ...-..|+|| |. +.|+ ..|.+ +|....
T Consensus 51 HATNSELLCEAFLHA~TGQPL--P~----D~Dl~Kd~~d~-ip~~ak 90 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPL--PD----DEDLRKERSDE-IPEAAK 90 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCC--CC----hhhhhhcCccc-chHHHH
Confidence 4578899999 8888899999 53 5677 77777 887664
No 9
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=16.07 E-value=64 Score=23.05 Aligned_cols=31 Identities=13% Similarity=0.348 Sum_probs=22.8
Q ss_pred cCeEEEEEEeCCCCCCCCCCEEEEEEEEcC-CccCC
Q 030306 136 TDWNMTEYRLLKHSCTSLDSWVLCKIYWES-EIIEN 170 (179)
Q Consensus 136 T~W~M~EY~l~~~~~~~~~~~VLCrI~~k~-~~~~~ 170 (179)
..-.|+||.+... ...|.||.|--.. +.|++
T Consensus 29 v~lal~eFgi~~~----s~~~sLceVtV~~~g~IKQ 60 (85)
T cd01785 29 VMLALQEFGITAP----SSNFSLCEVSVTPGGVIKQ 60 (85)
T ss_pred HHHHHHHhCCCCC----ccceEEEEEEecCCceeee
Confidence 4567889999886 4789999998654 44443
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=15.59 E-value=1.4e+02 Score=24.47 Aligned_cols=21 Identities=29% Similarity=0.368 Sum_probs=17.6
Q ss_pred ccCCChHHHHHH---HHHhhcCCCC
Q 030306 5 PYNPFDQSLIKQ---LNNKIIDEPV 26 (179)
Q Consensus 5 RF~PTDeELI~~---L~~Ki~g~pl 26 (179)
||. +|++||.| |.+|..|...
T Consensus 3 RF~-sDe~Li~yY~~L~K~~g~~~~ 26 (186)
T PF04700_consen 3 RFE-SDEELIEYYANLEKKYGGSDV 26 (186)
T ss_pred ccc-cHHHHHHHHHHHHHHhCCCCC
Confidence 443 79999999 8899998887
Done!