Query 046948
Match_columns 315
No_of_seqs 193 out of 954
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:07:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046948.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046948hhsearch_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 2.1E-42 4.6E-47 291.0 6.4 128 23-153 1-129 (129)
2 COG0618 Exopolyphosphatase-rel 22.3 71 0.0015 31.1 2.7 39 4-45 109-148 (332)
3 smart00265 BH4 BH4 Bcl-2 homol 21.0 1.1E+02 0.0023 19.5 2.3 20 32-51 4-23 (27)
4 PHA00692 hypothetical protein 16.1 47 0.001 25.0 -0.1 10 21-30 35-44 (74)
5 PF07960 CBP4: CBP4; InterPro 15.5 79 0.0017 27.2 1.1 11 30-40 30-40 (128)
6 KOG4286 Dystrophin-like protei 13.9 48 0.001 36.3 -0.7 26 132-157 634-659 (966)
7 smart00707 RPEL Repeat in Dros 13.4 1.2E+02 0.0027 19.0 1.3 14 26-39 6-19 (26)
8 PF02180 BH4: Bcl-2 homology r 12.0 2.1E+02 0.0046 18.2 2.0 19 33-51 5-23 (27)
9 KOG3238 Chloride ion current i 11.8 2.6E+02 0.0056 26.0 3.4 45 23-68 109-154 (216)
10 cd00952 CHBPH_aldolase Trans-o 11.8 1.3E+02 0.0029 28.8 1.7 20 21-40 107-126 (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=2.1e-42 Score=290.97 Aligned_cols=128 Identities=51% Similarity=0.976 Sum_probs=96.6
Q ss_pred CCCCceecCChHHHHHHHHHHHHcCCCCCC-CceeeccCCCCCCCCCCCcCCCCCceEEEEeecccccCCCCCCcccccC
Q 046948 23 QLPGFRFHPTDEELVGFYLRRKVDKKPLSI-ELIKQIDIYKHDPWDLPKISSTPDNEGYFFCKRGRKYRNSVRPNRVTGS 101 (315)
Q Consensus 23 lpPGfRF~PTDeELV~~YL~~Ki~g~plp~-~~I~~vDVY~~ePwdLp~~~~~ge~ewYFFs~r~rk~~~g~R~~R~tg~ 101 (315)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+|++....++.+|||||++.+++.++.|.+|++++
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 689999999999999999999999999987 8999999999999999954334667999999999999999999999999
Q ss_pred ceEeeecCceeEEcCCCCCceeeEEEEEEEeeeccCCCCCCcCeeEEEEeCC
Q 046948 102 GFWKATGIDKPVYSDGGEGQDCIGLKKTLVYYRGTAGKGTKTDWMMNEFRLP 153 (315)
Q Consensus 102 G~WK~~G~~k~I~~~~g~~~~vIG~Kktl~Fy~g~~~~g~kT~W~MhEY~L~ 153 (315)
|+||++|+.++|.+. ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~---~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDP---GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE----TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccc---cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999986 3789999999999998888899999999999984
No 2
>COG0618 Exopolyphosphatase-related proteins [General function prediction only]
Probab=22.28 E-value=71 Score=31.07 Aligned_cols=39 Identities=23% Similarity=0.094 Sum_probs=25.8
Q ss_pred ccccccccCC-CCCCccCCCCCCCceecCChHHHHHHHHHHHH
Q 046948 4 QNIKIDHHCY-RDDHEADDRQLPGFRFHPTDEELVGFYLRRKV 45 (315)
Q Consensus 4 ~~~~~~~~~~-~~~~~~~~~lpPGfRF~PTDeELV~~YL~~Ki 45 (315)
.-++||||+. .+...+-...-| -.++..|+|..||+..-
T Consensus 109 ~~ivIDHH~~~~~~~~~~~~i~~---~~~ataeii~~~~~~~~ 148 (332)
T COG0618 109 KVIVIDHHPGNNDIYGDFVWIDP---SAGATAEIIAELLKEAG 148 (332)
T ss_pred ceEEEeCCCCCCCCCCceEEeCC---CCchHHHHHHHHHHHcC
Confidence 3578999995 444443333333 34789999998887643
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=21.01 E-value=1.1e+02 Score=19.50 Aligned_cols=20 Identities=25% Similarity=0.331 Sum_probs=15.6
Q ss_pred ChHHHHHHHHHHHHcCCCCC
Q 046948 32 TDEELVGFYLRRKVDKKPLS 51 (315)
Q Consensus 32 TDeELV~~YL~~Ki~g~plp 51 (315)
+-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999655443
No 4
>PHA00692 hypothetical protein
Probab=16.12 E-value=47 Score=24.99 Aligned_cols=10 Identities=50% Similarity=0.833 Sum_probs=7.5
Q ss_pred CCCCCCceec
Q 046948 21 DRQLPGFRFH 30 (315)
Q Consensus 21 ~~lpPGfRF~ 30 (315)
..-||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 3457999995
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=15.45 E-value=79 Score=27.20 Aligned_cols=11 Identities=55% Similarity=0.827 Sum_probs=9.6
Q ss_pred cCChHHHHHHH
Q 046948 30 HPTDEELVGFY 40 (315)
Q Consensus 30 ~PTDeELV~~Y 40 (315)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 6
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=13.86 E-value=48 Score=36.34 Aligned_cols=26 Identities=31% Similarity=0.634 Sum_probs=21.9
Q ss_pred eeeccCCCCCCcCeeEEEEeCCCCCC
Q 046948 132 YYRGTAGKGTKTDWMMNEFRLPSDDR 157 (315)
Q Consensus 132 Fy~g~~~~g~kT~W~MhEY~L~~~~~ 157 (315)
|..|+++++.+++.-|.||..+....
T Consensus 634 F~sgraak~hk~~~pM~Ey~~~tts~ 659 (966)
T KOG4286|consen 634 FFSGRAAKGHKMHYPMVEYCTPTTSG 659 (966)
T ss_pred hhhcccccCCCCCCCceeeeCCCCCh
Confidence 34688899999999999999887654
No 7
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=13.40 E-value=1.2e+02 Score=18.99 Aligned_cols=14 Identities=36% Similarity=0.330 Sum_probs=11.1
Q ss_pred CceecCChHHHHHH
Q 046948 26 GFRFHPTDEELVGF 39 (315)
Q Consensus 26 GfRF~PTDeELV~~ 39 (315)
....+||.+|||..
T Consensus 6 kl~~RP~~eeLv~r 19 (26)
T smart00707 6 KLSQRPTREELEER 19 (26)
T ss_pred HHHcCCCHHHHHHc
Confidence 34678999999974
No 8
>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=12.00 E-value=2.1e+02 Score=18.17 Aligned_cols=19 Identities=26% Similarity=0.422 Sum_probs=14.9
Q ss_pred hHHHHHHHHHHHHcCCCCC
Q 046948 33 DEELVGFYLRRKVDKKPLS 51 (315)
Q Consensus 33 DeELV~~YL~~Ki~g~plp 51 (315)
-.|||.+|+.-|+.-...+
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 4799999999999655444
No 9
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=11.79 E-value=2.6e+02 Score=26.01 Aligned_cols=45 Identities=20% Similarity=0.395 Sum_probs=25.0
Q ss_pred CCCCceecCChHHHHHHHHHHHH-cCCCCCCCceeeccCCCCCCCCC
Q 046948 23 QLPGFRFHPTDEELVGFYLRRKV-DKKPLSIELIKQIDIYKHDPWDL 68 (315)
Q Consensus 23 lpPGfRF~PTDeELV~~YL~~Ki-~g~plp~~~I~~vDVY~~ePwdL 68 (315)
..-+|||+|+|.--+.. +..-+ ....+-+....+.+-|.-+=|+.
T Consensus 109 ~i~e~rfvpsDk~~l~a-~f~qfcecqel~p~P~ED~~~~dgee~~m 154 (216)
T KOG3238|consen 109 PITEFRFVPSDKSALEA-MFTQFCECQELNPDPDEDEDDYDGEEYDM 154 (216)
T ss_pred ccccceecCCchhHHHH-HHHHHHhhhhcCCCccccccccccchhhh
Confidence 33599999999877765 33322 33333222244555555555554
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=11.77 E-value=1.3e+02 Score=28.83 Aligned_cols=20 Identities=15% Similarity=0.071 Sum_probs=14.9
Q ss_pred CCCCCCceecCChHHHHHHH
Q 046948 21 DRQLPGFRFHPTDEELVGFY 40 (315)
Q Consensus 21 ~~lpPGfRF~PTDeELV~~Y 40 (315)
.++.|=|.|.||++||+.||
T Consensus 107 vlv~~P~y~~~~~~~l~~yf 126 (309)
T cd00952 107 TMLGRPMWLPLDVDTAVQFY 126 (309)
T ss_pred EEECCCcCCCCCHHHHHHHH
Confidence 33344477999999999976
Done!