Query 019821
Match_columns 335
No_of_seqs 184 out of 1000
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 04:48:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019821.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019821hhsearch_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 1.3E-42 2.9E-47 294.3 7.4 127 8-137 1-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 24.4 86 0.0019 20.4 2.5 20 17-36 4-23 (27)
3 PHA00692 hypothetical protein 16.7 56 0.0012 25.2 0.4 9 7-15 36-44 (74)
4 smart00707 RPEL Repeat in Dros 14.0 1E+02 0.0022 19.9 1.1 14 11-24 6-19 (26)
5 PF02180 BH4: Bcl-2 homology r 13.0 2.2E+02 0.0048 18.6 2.4 19 18-36 5-23 (27)
6 PF07960 CBP4: CBP4; InterPro 12.9 1E+02 0.0022 27.0 1.1 11 15-25 30-40 (128)
7 PLN02417 dihydrodipicolinate s 12.1 1.4E+02 0.0031 28.5 2.0 18 8-26 103-120 (280)
8 PF14599 zinc_ribbon_6: Zinc-r 11.5 79 0.0017 24.2 0.0 16 286-301 4-19 (61)
9 PF07131 DUF1382: Protein of u 11.2 1.6E+02 0.0034 22.7 1.5 14 10-23 22-39 (61)
10 cd00952 CHBPH_aldolase Trans-o 10.9 1.7E+02 0.0036 28.6 2.0 17 8-25 110-126 (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=1.3e-42 Score=294.32 Aligned_cols=127 Identities=51% Similarity=1.072 Sum_probs=96.6
Q ss_pred CCCCceeCCChHHHHHHHHHHHHccCCCCC-CeeeeccCCCCCCchhhhhhcCCCCCCCeEEEEeecCCCCCCCCccccc
Q 019821 8 VPPGFRFHPTEEELVGYYLKRKINSLKIDL-DVIIDIDLYKIEPWDIQARCNLGYDEQNEWYFFSHKDRKYPTGTRTNRA 86 (335)
Q Consensus 8 LPPGfRF~PTDEELV~~YLr~Kv~g~pl~~-~vI~dvDVY~~ePwdL~~~~~~G~~~~~eWYFFs~r~kK~~~G~R~nRa 86 (335)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||+.|||+|++.... .+++||||+++++++.++.|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~---~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKG---GDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS----SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccC---CCceEEEEEecccccCCccccccc
Confidence 799999999999999999999999999877 7999999999999999953222 346999999999999999999999
Q ss_pred CCCCeeeecCCCeEEec-CCeEEEeEEEEeeeccCCCCCCCcCeEEEEEEeC
Q 019821 87 TAAGFWKATGRDKAVLS-KNKLIGMRKTLVFYKGRAPNGSKTDWIMHEYRLQ 137 (335)
Q Consensus 87 tggG~WK~tG~~k~I~~-~G~vIG~KKtLvFy~gr~p~g~KT~WiMhEYrL~ 137 (335)
+++|+||++|+.++|.+ +|.+||+|++|+||.++.+++.+|+|+||||+|+
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 99999999999999996 8999999999999998888999999999999984
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=24.37 E-value=86 Score=20.43 Aligned_cols=20 Identities=25% Similarity=0.320 Sum_probs=15.8
Q ss_pred ChHHHHHHHHHHHHccCCCC
Q 019821 17 TEEELVGYYLKRKINSLKID 36 (335)
Q Consensus 17 TDEELV~~YLr~Kv~g~pl~ 36 (335)
+-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999755443
No 3
>PHA00692 hypothetical protein
Probab=16.69 E-value=56 Score=25.22 Aligned_cols=9 Identities=67% Similarity=1.412 Sum_probs=6.8
Q ss_pred CCCCCceeC
Q 019821 7 SVPPGFRFH 15 (335)
Q Consensus 7 ~LPPGfRF~ 15 (335)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 358899885
No 4
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=14.00 E-value=1e+02 Score=19.86 Aligned_cols=14 Identities=36% Similarity=0.380 Sum_probs=11.4
Q ss_pred CceeCCChHHHHHH
Q 019821 11 GFRFHPTEEELVGY 24 (335)
Q Consensus 11 GfRF~PTDEELV~~ 24 (335)
...++||.||||.-
T Consensus 6 kl~~RP~~eeLv~r 19 (26)
T smart00707 6 KLSQRPTREELEER 19 (26)
T ss_pred HHHcCCCHHHHHHc
Confidence 45689999999974
No 5
>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=12.97 E-value=2.2e+02 Score=18.59 Aligned_cols=19 Identities=26% Similarity=0.314 Sum_probs=14.9
Q ss_pred hHHHHHHHHHHHHccCCCC
Q 019821 18 EEELVGYYLKRKINSLKID 36 (335)
Q Consensus 18 DEELV~~YLr~Kv~g~pl~ 36 (335)
-.|||.+|+.-|+.-...+
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 4799999999999755543
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=12.93 E-value=1e+02 Score=27.03 Aligned_cols=11 Identities=64% Similarity=0.896 Sum_probs=9.5
Q ss_pred CCChHHHHHHH
Q 019821 15 HPTEEELVGYY 25 (335)
Q Consensus 15 ~PTDEELV~~Y 25 (335)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 7
>PLN02417 dihydrodipicolinate synthase
Probab=12.13 E-value=1.4e+02 Score=28.51 Aligned_cols=18 Identities=17% Similarity=0.384 Sum_probs=14.5
Q ss_pred CCCCceeCCChHHHHHHHH
Q 019821 8 VPPGFRFHPTEEELVGYYL 26 (335)
Q Consensus 8 LPPGfRF~PTDEELV~~YL 26 (335)
+|| +.|.||++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 456 568999999999874
No 8
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=11.48 E-value=79 Score=24.19 Aligned_cols=16 Identities=19% Similarity=0.356 Sum_probs=0.0
Q ss_pred cccchhhHhHHHHhhh
Q 019821 286 NVTDWKNLDNLLESQV 301 (335)
Q Consensus 286 ~~~dw~~ld~~~asql 301 (335)
+..-||.||+-+|+|-
T Consensus 4 M~~~w~~LD~~i~~~p 19 (61)
T PF14599_consen 4 MSAYWRMLDAEIAATP 19 (61)
T ss_dssp ----------------
T ss_pred HHHHHHHHHHHHHhCC
Confidence 3467999999999975
No 9
>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=11.16 E-value=1.6e+02 Score=22.74 Aligned_cols=14 Identities=50% Similarity=0.800 Sum_probs=11.0
Q ss_pred CCceeCC----ChHHHHH
Q 019821 10 PGFRFHP----TEEELVG 23 (335)
Q Consensus 10 PGfRF~P----TDEELV~ 23 (335)
.|+||.| ||+|...
T Consensus 22 ~GIRFVpiPv~~dee~~~ 39 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHT 39 (61)
T ss_pred cCceeeccccccHHHHHH
Confidence 5999998 7777654
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=10.92 E-value=1.7e+02 Score=28.58 Aligned_cols=17 Identities=18% Similarity=0.331 Sum_probs=14.2
Q ss_pred CCCCceeCCChHHHHHHH
Q 019821 8 VPPGFRFHPTEEELVGYY 25 (335)
Q Consensus 8 LPPGfRF~PTDEELV~~Y 25 (335)
+|| |.|.||++||+.||
T Consensus 110 ~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 110 GRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred CCC-cCCCCCHHHHHHHH
Confidence 566 66899999999986
Done!