Query 033258
Match_columns 123
No_of_seqs 111 out of 794
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 11:44:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033258.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033258hhsearch_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 5E-32 1.1E-36 187.0 7.3 93 1-95 37-129 (129)
2 PF01473 CW_binding_1: Putativ 41.5 21 0.00046 15.9 1.3 8 19-26 7-14 (19)
3 cd01785 PDZ_GEF_RA Ubiquitin-l 29.2 18 0.00038 23.2 -0.1 13 85-97 29-41 (85)
4 KOG3761 Choline transporter [L 20.8 29 0.00063 28.5 -0.3 21 82-102 299-319 (591)
5 PF09866 DUF2093: Uncharacteri 20.3 81 0.0018 17.6 1.5 11 112-122 4-14 (42)
6 COG3908 Uncharacterized protei 17.9 1.3E+02 0.0029 18.7 2.2 10 112-121 27-36 (77)
7 PF08018 Antimicrobial_1: Frog 14.2 30 0.00066 16.9 -1.0 8 116-123 16-23 (24)
8 PF13389 DUF4107: Protein of u 13.6 1.5E+02 0.0032 20.9 1.8 23 7-29 120-142 (158)
9 PF04839 PSRP-3_Ycf65: Plastid 12.4 99 0.0021 17.8 0.6 7 23-29 4-10 (49)
10 COG3323 Uncharacterized protei 11.5 3E+02 0.0065 18.5 2.8 20 42-61 43-62 (109)
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=99.97 E-value=5e-32 Score=187.05 Aligned_cols=93 Identities=30% Similarity=0.586 Sum_probs=68.1
Q ss_pred CCCCCCCCCCccccccCCCceEEEeeecccCCCCCCcceeeecccEEeecCCCeeEEcCCCceEEEEEEEEEEEeecCCC
Q 033258 1 MDLSTFDPNDVVFDERCRANETYFYAWLVNKRGKGMVQRVVTKRGYWEADGVDVPVYSDREMKVMVGFKKNWTFYLGTEP 80 (123)
Q Consensus 1 vDvy~~~Pw~L~~~~~~~~~~wyFF~~~~~k~~~g~r~~R~~~~G~Wk~~g~~~~I~~~~g~~~~vG~kk~l~Fy~g~~~ 80 (123)
+|||+.|||+|+.....++++||||+++..++.++.|.+|++++|+||++|++++|.+.++ .+||+|++|+||.++.+
T Consensus 37 ~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~~i~~~~g--~~iG~k~~l~f~~~~~~ 114 (129)
T PF02365_consen 37 VDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDPGG--KVIGFKKTLVFYSGKSP 114 (129)
T ss_dssp --GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETTEEEEEECEEEEEEE-TT--CEEEEEEEEEEEESSTT
T ss_pred cccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccceEEeecccccccccccc--eeeeeEEEEEEEeccCC
Confidence 6999999999995333357899999999999999999999999999999999999998643 68999999999998888
Q ss_pred CCCccCeEEEEEEeC
Q 033258 81 EGQKSAWSMTEYRVN 95 (123)
Q Consensus 81 ~~~kt~W~MhEY~l~ 95 (123)
++.+|+|+||||+|.
T Consensus 115 ~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 115 NGKKTGWVMHEYSLE 129 (129)
T ss_dssp S-EEEEEEEEEEEE-
T ss_pred CCCcCCeEEEEEEeC
Confidence 899999999999984
No 2
>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=41.51 E-value=21 Score=15.91 Aligned_cols=8 Identities=13% Similarity=0.634 Sum_probs=6.4
Q ss_pred CceEEEee
Q 033258 19 ANETYFYA 26 (123)
Q Consensus 19 ~~~wyFF~ 26 (123)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899994
No 3
>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=29.15 E-value=18 Score=23.18 Aligned_cols=13 Identities=8% Similarity=0.314 Sum_probs=7.5
Q ss_pred cCeEEEEEEeCCC
Q 033258 85 SAWSMTEYRVNPR 97 (123)
Q Consensus 85 t~W~MhEY~l~~~ 97 (123)
+.--|+||.|...
T Consensus 29 v~lal~eFgi~~~ 41 (85)
T cd01785 29 VMLALQEFGITAP 41 (85)
T ss_pred HHHHHHHhCCCCC
Confidence 3444667766654
No 4
>KOG3761 consensus Choline transporter [Lipid transport and metabolism]
Probab=20.81 E-value=29 Score=28.45 Aligned_cols=21 Identities=19% Similarity=0.457 Sum_probs=17.5
Q ss_pred CCccCeEEEEEEeCCCCCCCC
Q 033258 82 GQKSAWSMTEYRVNPRLIPAD 102 (123)
Q Consensus 82 ~~kt~W~MhEY~l~~~~~~~~ 102 (123)
+..|+|-|..|.+.++.....
T Consensus 299 ~~ntdw~~t~y~~~d~~tkve 319 (591)
T KOG3761|consen 299 AANTDWNMTAYGLPDNGTKVE 319 (591)
T ss_pred hccCcccccccCCCCCCcccc
Confidence 568999999999999876544
No 5
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.31 E-value=81 Score=17.59 Aligned_cols=11 Identities=27% Similarity=0.459 Sum_probs=8.8
Q ss_pred CCcEEEEEEee
Q 033258 112 IVSYAVCKITK 122 (123)
Q Consensus 112 ~~~~VlCrI~~ 122 (123)
.++||+|-|-.
T Consensus 4 pG~~V~CAVTg 14 (42)
T PF09866_consen 4 PGSFVRCAVTG 14 (42)
T ss_pred CCCEEEEEeeC
Confidence 48899998853
No 6
>COG3908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=17.95 E-value=1.3e+02 Score=18.66 Aligned_cols=10 Identities=30% Similarity=0.667 Sum_probs=7.8
Q ss_pred CCcEEEEEEe
Q 033258 112 IVSYAVCKIT 121 (123)
Q Consensus 112 ~~~~VlCrI~ 121 (123)
.+.+|||-|-
T Consensus 27 ~GsfV~CAVt 36 (77)
T COG3908 27 PGSFVLCAVT 36 (77)
T ss_pred CCcEEEEEec
Confidence 3789999874
No 7
>PF08018 Antimicrobial_1: Frog antimicrobial peptide ; InterPro: IPR012520 This family includes antimicrobial peptides secreted from skins of frogs. The secretion of antimicrobial peptides from the skins of frogs plays an important role in the self defence of these frogs. Structural characterisation of these peptides showed that they belonged to four known families: the brevinin-1 family, the esculentin-2 family, the ranatuerin-2 family and the temporin family [].; GO: 0005576 extracellular region
Probab=14.21 E-value=30 Score=16.95 Aligned_cols=8 Identities=50% Similarity=0.820 Sum_probs=5.0
Q ss_pred EEEEEeeC
Q 033258 116 AVCKITKA 123 (123)
Q Consensus 116 VlCrI~~r 123 (123)
++|+|.|+
T Consensus 16 i~C~ItKK 23 (24)
T PF08018_consen 16 IFCAITKK 23 (24)
T ss_pred hHhhhccc
Confidence 56777653
No 8
>PF13389 DUF4107: Protein of unknown function (DUF4107)
Probab=13.60 E-value=1.5e+02 Score=20.93 Aligned_cols=23 Identities=22% Similarity=0.417 Sum_probs=15.8
Q ss_pred CCCCccccccCCCceEEEeeecc
Q 033258 7 DPNDVVFDERCRANETYFYAWLV 29 (123)
Q Consensus 7 ~Pw~L~~~~~~~~~~wyFF~~~~ 29 (123)
.|-+-|.+.+.|...||-|.+|.
T Consensus 120 ~~yeRpFDPktGGSNWyHYGrr~ 142 (158)
T PF13389_consen 120 NPYERPFDPKTGGSNWYHYGRRR 142 (158)
T ss_pred CccCCCCCCCcCCccceecchhh
Confidence 34444555666788999997775
No 9
>PF04839 PSRP-3_Ycf65: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65); InterPro: IPR006924 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome, 0009536 plastid; PDB: 2KT9_A.
Probab=12.42 E-value=99 Score=17.84 Aligned_cols=7 Identities=29% Similarity=0.344 Sum_probs=4.9
Q ss_pred EEeeecc
Q 033258 23 YFYAWLV 29 (123)
Q Consensus 23 yFF~~~~ 29 (123)
|||-||.
T Consensus 4 yfFWPr~ 10 (49)
T PF04839_consen 4 YFFWPRE 10 (49)
T ss_dssp -EEETTS
T ss_pred cccCCCC
Confidence 8888886
No 10
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=11.45 E-value=3e+02 Score=18.53 Aligned_cols=20 Identities=10% Similarity=0.077 Sum_probs=15.8
Q ss_pred ecccEEeecCCCeeEEcCCC
Q 033258 42 TKRGYWEADGVDVPVYSDRE 61 (123)
Q Consensus 42 ~~~G~Wk~~g~~~~I~~~~g 61 (123)
.+.|+|++-++..|....-|
T Consensus 43 ~g~G~frP~egAnP~iGevg 62 (109)
T COG3323 43 EGTGQFRPLEGANPFIGEVG 62 (109)
T ss_pred eeeEEEeecCCCCCcccccc
Confidence 46799999998888886554
Done!