Query 042376
Match_columns 357
No_of_seqs 146 out of 955
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 05:38:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042376hhsearch_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 2.5E-41 5.3E-46 288.5 8.1 127 8-137 1-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 20.4 1.1E+02 0.0024 20.3 2.4 20 17-36 4-23 (27)
3 KOG3191 Predicted N6-DNA-methy 13.1 90 0.0019 29.8 0.9 45 283-332 117-165 (209)
4 PHA00692 hypothetical protein 13.0 79 0.0017 24.8 0.4 8 8-15 37-44 (74)
5 PF07960 CBP4: CBP4; InterPro 12.9 1E+02 0.0022 27.4 1.2 14 12-25 26-40 (128)
6 COG1803 MgsA Methylglyoxal syn 10.9 97 0.0021 27.9 0.3 46 257-307 27-75 (142)
7 PF08338 DUF1731: Domain of un 10.7 1.8E+02 0.0039 21.2 1.6 17 10-26 31-48 (48)
8 PF01473 CW_binding_1: Putativ 10.4 1.8E+02 0.0039 16.9 1.3 8 64-71 7-14 (19)
9 PF02180 BH4: Bcl-2 homology r 10.3 2.4E+02 0.0053 18.7 2.0 19 18-36 5-23 (27)
10 smart00707 RPEL Repeat in Dros 9.7 1.9E+02 0.0042 18.9 1.3 13 11-23 6-18 (26)
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=2.5e-41 Score=288.48 Aligned_cols=127 Identities=51% Similarity=1.062 Sum_probs=96.5
Q ss_pred CCCCceeCCChHHHHHHHHHHHHcCCCCCc-cceeeecCCCCCChhhhhhhccCCCCCCeeEEEeecCCcCCCCCccccc
Q 042376 8 VPPGFRFHPTDEELLHYYLRKKVSFQKFDM-EVIREVDLNKMEPWELQERCRIGSTPQNEWYFFSHKDRKYPTGSRTNRA 86 (357)
Q Consensus 8 LPPGfRF~PTDEELI~~YLr~KI~g~pl~~-~vI~evDVY~~ePweLp~~~~~g~~~d~eWYFFspr~rK~~~GsR~~Ra 86 (357)
|||||||+|||+|||.+||++|+.+.+++. ++|.++|||++|||+|+.... ..+++||||+++++++.++.|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~---~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFK---GGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSS---S-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhcc---CCCceEEEEEecccccCCccccccc
Confidence 899999999999999999999999999886 799999999999999995322 2467999999999999999999999
Q ss_pred cCCCeeeecCCCeEEec-CCeeeeeEEEEEEeeCCCCCCCCcCeEEEEEEeC
Q 042376 87 TNAGFWKATGRDKCIRN-SYKKIGMRKTLVFYRGRAPHGQKSDWIMHEYRLE 137 (357)
Q Consensus 87 tggG~WK~tG~~K~I~~-~g~vIG~KKtLvFY~gr~p~g~KTgWvMhEYrL~ 137 (357)
+++|+||.+|+.+.|.+ ++++||+|++|+||.++.+.+.+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999999987 8999999999999998888889999999999984
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=20.35 E-value=1.1e+02 Score=20.30 Aligned_cols=20 Identities=25% Similarity=0.443 Sum_probs=15.9
Q ss_pred ChHHHHHHHHHHHHcCCCCC
Q 042376 17 TDEELLHYYLRKKVSFQKFD 36 (357)
Q Consensus 17 TDEELI~~YLr~KI~g~pl~ 36 (357)
+-.|||.+|+.-|+..+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999998766544
No 3
>KOG3191 consensus Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=13.08 E-value=90 Score=29.81 Aligned_cols=45 Identities=29% Similarity=0.451 Sum_probs=35.7
Q ss_pred CCCceeeccCCCcccccchhccCCCCCCCCCchhhhhcccc--c--cCCCcccc
Q 042376 283 EPGLEVGTCEPTATHQMVAATTGGRDGQGLNDWTMLDRLVT--E--DSSKGVTF 332 (357)
Q Consensus 283 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~--~~~~~~~~ 332 (357)
.|+..+-+|++-+-++++.|-+||+++ =..+|+|.. + =|.+|+-+
T Consensus 117 NPPYVpt~~~~i~~~~i~~a~aGG~~G-----r~v~d~ll~~v~~iLSp~Gv~Y 165 (209)
T KOG3191|consen 117 NPPYVPTSDEEIGDEGIASAWAGGKDG-----REVTDRLLPQVPDILSPRGVFY 165 (209)
T ss_pred CCCcCcCCcccchhHHHHHHHhcCcch-----HHHHHHHHhhhhhhcCcCceEE
Confidence 789999999998889999999999973 234888775 2 26778765
No 4
>PHA00692 hypothetical protein
Probab=13.00 E-value=79 Score=24.77 Aligned_cols=8 Identities=75% Similarity=1.580 Sum_probs=6.4
Q ss_pred CCCCceeC
Q 042376 8 VPPGFRFH 15 (357)
Q Consensus 8 LPPGfRF~ 15 (357)
.||||||-
T Consensus 37 yppgfrfg 44 (74)
T PHA00692 37 YPPGFRFG 44 (74)
T ss_pred cCCCcccc
Confidence 58899885
No 5
>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=12.91 E-value=1e+02 Score=27.37 Aligned_cols=14 Identities=43% Similarity=0.956 Sum_probs=10.6
Q ss_pred cee-CCChHHHHHHH
Q 042376 12 FRF-HPTDEELLHYY 25 (357)
Q Consensus 12 fRF-~PTDEELI~~Y 25 (357)
|++ .||||||+..|
T Consensus 26 ~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 26 VKYTTPTEEELFKRY 40 (128)
T ss_pred heecCCCHHHHHHhc
Confidence 444 49999999765
No 6
>COG1803 MgsA Methylglyoxal synthase [Carbohydrate transport and metabolism]
Probab=10.91 E-value=97 Score=27.87 Aligned_cols=46 Identities=26% Similarity=0.318 Sum_probs=35.3
Q ss_pred HHhhhcCCCCccCCcccccccccccCCCCceeeccCCC---cccccchhccCCC
Q 042376 257 KQLMSNTSRDCESGSENLRYHHQQACEPGLEVGTCEPT---ATHQMVAATTGGR 307 (357)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~ 307 (357)
|.+|++ +.-++.|.-+.+- |.+| ||+|-.-..| +-||.+|..+-|.
T Consensus 27 ~~~L~~-h~L~ATGTTG~~i--~~at--gL~v~~~~SGPmGGDQQiGa~Iaeg~ 75 (142)
T COG1803 27 KELLSR-HDLYATGTTGGLI--QEAT--GLNVHRLKSGPMGGDQQIGALIAEGK 75 (142)
T ss_pred HHHhhh-ceEEEecCchHHH--HHHh--CCceEEeecCCCCccHHHHHHHhcCc
Confidence 567888 8888899988888 4777 9999876655 5677777666655
No 7
>PF08338 DUF1731: Domain of unknown function (DUF1731); InterPro: IPR013549 This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (IPR001509 from INTERPRO) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. ; PDB: 3OH8_A.
Probab=10.66 E-value=1.8e+02 Score=21.23 Aligned_cols=17 Identities=53% Similarity=0.802 Sum_probs=9.3
Q ss_pred CCceeC-CChHHHHHHHH
Q 042376 10 PGFRFH-PTDEELLHYYL 26 (357)
Q Consensus 10 PGfRF~-PTDEELI~~YL 26 (357)
-||+|+ |+-++-+.+.|
T Consensus 31 ~GF~F~~p~l~~AL~~ll 48 (48)
T PF08338_consen 31 AGFQFRYPTLEEALRDLL 48 (48)
T ss_dssp TT---S-SSHHHHHHH--
T ss_pred CCCcccCCCHHHHHhccC
Confidence 599998 88888776543
No 8
>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=10.36 E-value=1.8e+02 Score=16.89 Aligned_cols=8 Identities=38% Similarity=1.522 Sum_probs=6.2
Q ss_pred CCeeEEEe
Q 042376 64 QNEWYFFS 71 (357)
Q Consensus 64 d~eWYFFs 71 (357)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47899994
No 9
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=10.31 E-value=2.4e+02 Score=18.72 Aligned_cols=19 Identities=26% Similarity=0.441 Sum_probs=15.0
Q ss_pred hHHHHHHHHHHHHcCCCCC
Q 042376 18 DEELLHYYLRKKVSFQKFD 36 (357)
Q Consensus 18 DEELI~~YLr~KI~g~pl~ 36 (357)
-.|||.+|+.-|+.....+
T Consensus 5 nR~lV~~yi~yKLsQrgy~ 23 (27)
T PF02180_consen 5 NRELVEDYISYKLSQRGYV 23 (27)
T ss_dssp HHHHHHHHHHHHHHHTTST
T ss_pred HHHHHHHHHHHHhhhcCCC
Confidence 4799999999998765544
No 10
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=9.71 E-value=1.9e+02 Score=18.94 Aligned_cols=13 Identities=38% Similarity=0.445 Sum_probs=10.7
Q ss_pred CceeCCChHHHHH
Q 042376 11 GFRFHPTDEELLH 23 (357)
Q Consensus 11 GfRF~PTDEELI~ 23 (357)
...++|+.+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3568999999996
Done!