Query 025570
Match_columns 250
No_of_seqs 174 out of 950
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 07:11:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025570.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025570hhsearch_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 7.9E-37 1.7E-41 247.9 8.5 107 4-111 1-128 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 43.1 22 0.00047 21.6 1.9 15 13-27 4-18 (27)
3 PHA00692 hypothetical protein 40.2 11 0.00024 27.1 0.4 10 3-12 36-45 (74)
4 PF02180 BH4: Bcl-2 homology r 28.9 52 0.0011 20.0 1.9 14 14-27 5-18 (27)
5 PF07960 CBP4: CBP4; InterPro 26.8 33 0.00072 28.3 1.1 12 10-21 29-40 (128)
6 COG2326 Uncharacterized conser 23.1 43 0.00094 30.9 1.3 27 5-31 100-130 (270)
7 PLN02417 dihydrodipicolinate s 22.8 52 0.0011 29.9 1.7 17 4-21 103-119 (280)
8 cd00954 NAL N-Acetylneuraminic 21.4 57 0.0012 29.6 1.7 18 4-22 103-120 (288)
9 TIGR02313 HpaI-NOT-DapA 2,4-di 21.4 61 0.0013 29.7 1.9 17 4-21 102-118 (294)
10 cd00952 CHBPH_aldolase Trans-o 21.0 58 0.0013 30.1 1.7 17 4-21 110-126 (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=7.9e-37 Score=247.85 Aligned_cols=107 Identities=52% Similarity=1.050 Sum_probs=78.7
Q ss_pred CCCCcEEcCCHHHHHHHHHHHhhh---------------------hhhccccCCCCceEEEEccccccccCCCCCccccc
Q 025570 4 LPPGYRFFPTEEELVSFYLINKLE---------------------ELCGEKCQGDTEQWFFFTPRQEREERGGRPSRTTA 62 (250)
Q Consensus 4 LPpGfRF~PTDeELV~~YL~~Ki~---------------------~lp~~~~~g~~e~WYFFs~r~~k~~~G~R~~R~t~ 62 (250)
|||||||+|||+|||.+||++||. +|+. ...+.+++||||+++++++.++.|++|+++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~-~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~ 79 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPA-KFKGGDEEWYFFSPRKKKYPNGGRPNRVTG 79 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHH-HSSS-SSEEEEEEE----------S-EEET
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhh-hccCCCceEEEEEecccccCCccccccccc
Confidence 899999999999999999999998 2231 112345579999999999999999999999
Q ss_pred CceeEecCCCeeEEcCCCeEEEEEEEEeeecCcCCCCCCcCeEEEEEEe
Q 025570 63 SGYWKATGSPSYVYSSDNRVIGVKKTMVFYKGKAPTGRKTKWKMHEYRA 111 (250)
Q Consensus 63 ~G~Wk~tG~~k~V~~~~g~~IG~KktlvFy~g~~p~g~kT~WvMhEYrl 111 (250)
+|+||++|+.++|++.++.+||+|++|+||.++.+.+.+|+|+||||+|
T Consensus 80 ~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L 128 (129)
T PF02365_consen 80 GGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSL 128 (129)
T ss_dssp TEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE
T ss_pred ceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEe
Confidence 9999999999999987899999999999999888889999999999998
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=43.13 E-value=22 Score=21.63 Aligned_cols=15 Identities=40% Similarity=0.485 Sum_probs=13.1
Q ss_pred CHHHHHHHHHHHhhh
Q 025570 13 TEEELVSFYLINKLE 27 (250)
Q Consensus 13 TDeELV~~YL~~Ki~ 27 (250)
+-.|||.+|+.-||.
T Consensus 4 ~nRelV~~yv~yKLs 18 (27)
T smart00265 4 DNRELVVDYVTYKLS 18 (27)
T ss_pred chHHHHHHHHHHHHh
Confidence 457999999999986
No 3
>PHA00692 hypothetical protein
Probab=40.23 E-value=11 Score=27.12 Aligned_cols=10 Identities=60% Similarity=1.178 Sum_probs=7.6
Q ss_pred CCCCCcEEcC
Q 025570 3 ELPPGYRFFP 12 (250)
Q Consensus 3 ~LPpGfRF~P 12 (250)
..||||||--
T Consensus 36 eyppgfrfgg 45 (74)
T PHA00692 36 EYPPGFRFGG 45 (74)
T ss_pred ecCCCccccc
Confidence 4799999853
No 4
>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=28.86 E-value=52 Score=20.00 Aligned_cols=14 Identities=43% Similarity=0.544 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHhhh
Q 025570 14 EEELVSFYLINKLE 27 (250)
Q Consensus 14 DeELV~~YL~~Ki~ 27 (250)
-.|||.+|+.-||.
T Consensus 5 nR~lV~~yi~yKLs 18 (27)
T PF02180_consen 5 NRELVEDYISYKLS 18 (27)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhh
Confidence 47999999999986
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=26.79 E-value=33 Score=28.30 Aligned_cols=12 Identities=58% Similarity=0.703 Sum_probs=10.2
Q ss_pred EcCCHHHHHHHH
Q 025570 10 FFPTEEELVSFY 21 (250)
Q Consensus 10 F~PTDeELV~~Y 21 (250)
=.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 379999999975
No 6
>COG2326 Uncharacterized conserved protein [Function unknown]
Probab=23.06 E-value=43 Score=30.90 Aligned_cols=27 Identities=30% Similarity=0.475 Sum_probs=22.3
Q ss_pred CCCcEE----cCCHHHHHHHHHHHhhhhhhc
Q 025570 5 PPGYRF----FPTEEELVSFYLINKLEELCG 31 (250)
Q Consensus 5 PpGfRF----~PTDeELV~~YL~~Ki~~lp~ 31 (250)
|-|+|- -|||+|+-..||.+-+..||.
T Consensus 100 PR~~rvval~aPt~~E~~qwY~qRy~~~lPa 130 (270)
T COG2326 100 PRGARVVALPAPTDRERGQWYFQRYVAHLPA 130 (270)
T ss_pred CceeEEeecCCCChHhhccHHHHHHHHhCCC
Confidence 446663 499999999999999998874
No 7
>PLN02417 dihydrodipicolinate synthase
Probab=22.81 E-value=52 Score=29.89 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=14.2
Q ss_pred CCCCcEEcCCHHHHHHHH
Q 025570 4 LPPGYRFFPTEEELVSFY 21 (250)
Q Consensus 4 LPpGfRF~PTDeELV~~Y 21 (250)
+|| |.|.||++||+.||
T Consensus 103 ~~P-~y~~~~~~~i~~~f 119 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHF 119 (280)
T ss_pred cCC-ccCCCCHHHHHHHH
Confidence 456 55899999999998
No 8
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=21.44 E-value=57 Score=29.60 Aligned_cols=18 Identities=22% Similarity=0.346 Sum_probs=13.9
Q ss_pred CCCCcEEcCCHHHHHHHHH
Q 025570 4 LPPGYRFFPTEEELVSFYL 22 (250)
Q Consensus 4 LPpGfRF~PTDeELV~~YL 22 (250)
+||- .|.||++||+.||.
T Consensus 103 ~~P~-y~~~~~~~i~~~~~ 120 (288)
T cd00954 103 ITPF-YYKFSFEEIKDYYR 120 (288)
T ss_pred eCCC-CCCCCHHHHHHHHH
Confidence 3554 47899999999873
No 9
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=21.37 E-value=61 Score=29.69 Aligned_cols=17 Identities=29% Similarity=0.546 Sum_probs=14.0
Q ss_pred CCCCcEEcCCHHHHHHHH
Q 025570 4 LPPGYRFFPTEEELVSFY 21 (250)
Q Consensus 4 LPpGfRF~PTDeELV~~Y 21 (250)
+||-| |.|++++|+.||
T Consensus 102 ~pP~y-~~~~~~~l~~~f 118 (294)
T TIGR02313 102 IVPYY-NKPNQEALYDHF 118 (294)
T ss_pred cCccC-CCCCHHHHHHHH
Confidence 45554 899999999997
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=21.03 E-value=58 Score=30.09 Aligned_cols=17 Identities=24% Similarity=0.282 Sum_probs=14.4
Q ss_pred CCCCcEEcCCHHHHHHHH
Q 025570 4 LPPGYRFFPTEEELVSFY 21 (250)
Q Consensus 4 LPpGfRF~PTDeELV~~Y 21 (250)
+|| |.|.|+++||+.||
T Consensus 110 ~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 110 GRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred CCC-cCCCCCHHHHHHHH
Confidence 566 56899999999998
Done!