Query 029016
Match_columns 200
No_of_seqs 130 out of 954
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 06:08:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029016hhsearch_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 3.1E-43 6.7E-48 272.2 8.3 120 13-132 1-129 (129)
2 PF07491 PPI_Ypi1: Protein pho 49.6 14 0.00031 24.9 2.0 23 159-181 34-56 (60)
3 PHA00692 hypothetical protein 36.9 13 0.00028 25.1 0.3 10 11-20 35-44 (74)
4 smart00265 BH4 BH4 Bcl-2 homol 34.6 54 0.0012 18.6 2.5 20 22-41 4-23 (27)
5 cd05790 S1_Rrp40 S1_Rrp40: Rrp 27.6 74 0.0016 22.8 2.9 30 153-185 47-76 (86)
6 PF07960 CBP4: CBP4; InterPro 25.4 38 0.00082 26.4 1.1 11 20-30 30-40 (128)
7 PLN02417 dihydrodipicolinate s 23.1 54 0.0012 28.2 1.8 20 11-31 101-120 (280)
8 smart00707 RPEL Repeat in Dros 23.1 58 0.0013 18.3 1.3 13 16-28 6-18 (26)
9 PF02180 BH4: Bcl-2 homology r 21.1 1.2E+02 0.0027 17.1 2.4 20 22-41 4-23 (27)
10 cd00952 CHBPH_aldolase Trans-o 20.7 62 0.0014 28.3 1.8 20 10-30 107-126 (309)
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=3.1e-43 Score=272.24 Aligned_cols=120 Identities=46% Similarity=0.903 Sum_probs=96.5
Q ss_pred CCCCeEEcCCHHHHHHHHHHHHHhCCCCCC-CceecCCCCCCCCCCcccccccCCceEEEEeec--------ccceeccc
Q 029016 13 LPPGFRFCPTDEELLVHFLQRKVALLPCHP-DVIPDLDLYPYDPWQLNGKALAEGNQWYFYSRK--------TQNRMTGN 83 (200)
Q Consensus 13 LPpG~rF~PTDeELv~~YL~~k~~g~pl~~-~~I~~~Dvy~~~P~~L~~~~~~~~~~wyFF~~~--------r~~R~~g~ 83 (200)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||++|||+|+.....++++||||+++ |.+|++++
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 899999999999999999999999999887 799999999999999995434466799999997 46788999
Q ss_pred ceeeeCCcceeEEcCCceeEEEEEEEEeeeCCCCCCCccCeEEEEEEeC
Q 029016 84 GYWKPMGIEESVLTRADKKVGLKKYYIFHLGEASAGVKTNWIMQEYRLS 132 (200)
Q Consensus 84 G~Wk~~g~~k~I~~~~g~~vG~kr~f~F~~~~~~~~~kT~W~M~EY~l~ 132 (200)
|+||.+|+.+.|.+.+|.+||+|++|+||.++.+++.+|+|+||||+|.
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 9999999999998878999999999999998888889999999999983
No 2
>PF07491 PPI_Ypi1: Protein phosphatase inhibitor ; InterPro: IPR011107 These proteins include Ypi1, a novel Saccharomyces cerevisiae type 1 protein phosphatase inhibitor [] and ppp1r11/hcgv (O60927 from SWISSPROT), annotated as having protein phosphatase inhibitor activity [].
Probab=49.58 E-value=14 Score=24.92 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=16.2
Q ss_pred CceEEEEEEEeCCCCCCCCCCcc
Q 029016 159 SKWVICRVFERNCDDDDDGAELS 181 (200)
Q Consensus 159 ~~~VLCkIy~k~~~~~~~~~~~s 181 (200)
..-=+|-||.|++.-.+++++++
T Consensus 34 kkSK~CCIyhk~~~~~esSs~s~ 56 (60)
T PF07491_consen 34 KKSKCCCIYHKPRAFDESSSESS 56 (60)
T ss_pred ccCceeeeecCCCCCCCCccccc
Confidence 34458999999998666555443
No 3
>PHA00692 hypothetical protein
Probab=36.86 E-value=13 Score=25.07 Aligned_cols=10 Identities=70% Similarity=1.424 Sum_probs=8.5
Q ss_pred CCCCCCeEEc
Q 029016 11 VNLPPGFRFC 20 (200)
Q Consensus 11 ~~LPpG~rF~ 20 (200)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4789999995
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=34.64 E-value=54 Score=18.59 Aligned_cols=20 Identities=20% Similarity=0.346 Sum_probs=15.7
Q ss_pred CHHHHHHHHHHHHHhCCCCC
Q 029016 22 TDEELLVHFLQRKVALLPCH 41 (200)
Q Consensus 22 TDeELv~~YL~~k~~g~pl~ 41 (200)
+-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999765444
No 5
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=27.56 E-value=74 Score=22.84 Aligned_cols=30 Identities=33% Similarity=0.491 Sum_probs=22.1
Q ss_pred CCCCCCCceEEEEEEEeCCCCCCCCCCccchhh
Q 029016 153 NSKTDYSKWVICRVFERNCDDDDDGAELSCMDE 185 (200)
Q Consensus 153 ~~~~~~~~~VLCkIy~k~~~~~~~~~~~s~~~~ 185 (200)
.+..+.+++|+|||..-.++. ..+++|.+.
T Consensus 47 rp~L~~GDlV~ArV~~~~~~~---~~eLtc~~~ 76 (86)
T cd05790 47 RPNLNVGDLVYARVVKANRDM---EPELSCVDS 76 (86)
T ss_pred cccCCCCCEEEEEEEecCCCC---CeEEEEeCC
Confidence 345667999999997765542 368899884
No 6
>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=25.43 E-value=38 Score=26.36 Aligned_cols=11 Identities=45% Similarity=0.893 Sum_probs=9.6
Q ss_pred cCCHHHHHHHH
Q 029016 20 CPTDEELLVHF 30 (200)
Q Consensus 20 ~PTDeELv~~Y 30 (200)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999876
No 7
>PLN02417 dihydrodipicolinate synthase
Probab=23.11 E-value=54 Score=28.25 Aligned_cols=20 Identities=25% Similarity=0.474 Sum_probs=15.5
Q ss_pred CCCCCCeEEcCCHHHHHHHHH
Q 029016 11 VNLPPGFRFCPTDEELLVHFL 31 (200)
Q Consensus 11 ~~LPpG~rF~PTDeELv~~YL 31 (200)
+-+|| +.|.||+++|+.||-
T Consensus 101 ~~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 101 LHINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EEcCC-ccCCCCHHHHHHHHH
Confidence 34566 568999999999874
No 8
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=23.08 E-value=58 Score=18.26 Aligned_cols=13 Identities=38% Similarity=0.314 Sum_probs=10.8
Q ss_pred CeEEcCCHHHHHH
Q 029016 16 GFRFCPTDEELLV 28 (200)
Q Consensus 16 G~rF~PTDeELv~ 28 (200)
...++|+-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3568999999997
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=21.06 E-value=1.2e+02 Score=17.14 Aligned_cols=20 Identities=15% Similarity=0.252 Sum_probs=15.2
Q ss_pred CHHHHHHHHHHHHHhCCCCC
Q 029016 22 TDEELLVHFLQRKVALLPCH 41 (200)
Q Consensus 22 TDeELv~~YL~~k~~g~pl~ 41 (200)
.-.|||.+|+.-|+.-...+
T Consensus 4 ~nR~lV~~yi~yKLsQrgy~ 23 (27)
T PF02180_consen 4 DNRELVEDYISYKLSQRGYV 23 (27)
T ss_dssp HHHHHHHHHHHHHHHHTTST
T ss_pred cHHHHHHHHHHHHhhhcCCC
Confidence 34799999999998765544
No 10
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=20.73 E-value=62 Score=28.33 Aligned_cols=20 Identities=5% Similarity=0.032 Sum_probs=16.0
Q ss_pred CCCCCCCeEEcCCHHHHHHHH
Q 029016 10 NVNLPPGFRFCPTDEELLVHF 30 (200)
Q Consensus 10 ~~~LPpG~rF~PTDeELv~~Y 30 (200)
-+-+|| |.|.||+++|+.||
T Consensus 107 vlv~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 107 TMLGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred EEECCC-cCCCCCHHHHHHHH
Confidence 356677 66899999999977
Done!