Query 014260
Match_columns 428
No_of_seqs 196 out of 967
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 03:24:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014260.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014260hhsearch_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 7E-42 1.5E-46 299.9 7.3 127 15-144 1-129 (129)
2 PHA00692 hypothetical protein 22.1 35 0.00076 27.1 0.4 10 14-23 36-45 (74)
3 smart00265 BH4 BH4 Bcl-2 homol 19.0 1.2E+02 0.0027 20.4 2.4 20 24-43 4-23 (27)
4 COG3060 MetJ Transcriptional r 15.5 1E+02 0.0022 26.3 1.8 39 22-64 51-89 (105)
5 PLN02417 dihydrodipicolinate s 13.5 1.2E+02 0.0026 30.2 1.9 20 13-33 101-120 (280)
6 cd00490 Met_repressor_MetJ Met 12.8 1.8E+02 0.0039 25.0 2.5 39 22-64 50-88 (103)
7 cd00952 CHBPH_aldolase Trans-o 12.0 1.4E+02 0.003 30.2 1.9 19 13-32 108-126 (309)
8 PF12672 DUF3793: Protein of u 11.9 2.2E+02 0.0049 26.7 3.2 40 18-63 83-123 (176)
9 PF02180 BH4: Bcl-2 homology r 11.6 2.5E+02 0.0054 19.0 2.4 19 25-43 5-23 (27)
10 PRK05264 transcriptional repre 11.1 2.1E+02 0.0047 24.7 2.4 39 22-64 51-89 (105)
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=7e-42 Score=299.92 Aligned_cols=127 Identities=52% Similarity=1.052 Sum_probs=96.9
Q ss_pred CCCCceecCChHHHHHHHHHHHhccCCCCC-CceeeccCCCCCCchhhhhhccCCCCCCeeEEEecCCCCCCCCCccccc
Q 014260 15 VPPGFRFHPTEEELLHYYLRKKVAYEKIDL-DVIREVDLNKLEPWDIQEKCKIGSTPQNDWYFFSHKDKKYPTGTRTNRA 93 (428)
Q Consensus 15 LPpGfRF~PTDeELV~~YL~~Kv~g~pl~~-~~I~evDVy~~ePWdL~~~~~~gs~~e~eWYFFs~r~kK~~~G~R~nR~ 93 (428)
|||||||+|||+|||.+||++|+.|++++. .+|+++|||.+|||+|++.... .+++||||+++++++.+|.|.+|+
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 899999999999999999999999999887 7999999999999999953222 367999999999999999999999
Q ss_pred ccCceeeecCCCeEEec-CcEEEEEEEEEEeeeCCCCCCCCcCeEEEEEEeC
Q 014260 94 TAAGFWKATGRDKIIYS-GFRRIGLRKTLVFYKGRAPHGQKSDWIMHEYRLE 144 (428)
Q Consensus 94 tg~G~WK~tG~dk~I~~-~g~~IG~KktLvFy~gr~p~g~KT~WiMhEY~L~ 144 (428)
+++|+||.+|+++.|.. ++++||+||+|+||.++.+++.||+|+||||+|.
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 99999999999999988 8999999999999998888899999999999984
No 2
>PHA00692 hypothetical protein
Probab=22.11 E-value=35 Score=27.12 Aligned_cols=10 Identities=60% Similarity=1.268 Sum_probs=7.8
Q ss_pred CCCCCceecC
Q 014260 14 QVPPGFRFHP 23 (428)
Q Consensus 14 ~LPpGfRF~P 23 (428)
..||||||--
T Consensus 36 eyppgfrfgg 45 (74)
T PHA00692 36 EYPPGFRFGG 45 (74)
T ss_pred ecCCCccccc
Confidence 5799999953
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=19.04 E-value=1.2e+02 Score=20.41 Aligned_cols=20 Identities=20% Similarity=0.325 Sum_probs=15.8
Q ss_pred ChHHHHHHHHHHHhccCCCC
Q 014260 24 TEEELLHYYLRKKVAYEKID 43 (428)
Q Consensus 24 TDeELV~~YL~~Kv~g~pl~ 43 (428)
.-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999765443
No 4
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=15.47 E-value=1e+02 Score=26.27 Aligned_cols=39 Identities=26% Similarity=0.284 Sum_probs=31.5
Q ss_pred cCChHHHHHHHHHHHhccCCCCCCceeeccCCCCCCchhhhhh
Q 014260 22 HPTEEELLHYYLRKKVAYEKIDLDVIREVDLNKLEPWDIQEKC 64 (428)
Q Consensus 22 ~PTDeELV~~YL~~Kv~g~pl~~~~I~evDVy~~ePWdL~~~~ 64 (428)
|-|..||++.-...-..|+|+| .+.|+.+.-|.+||+..
T Consensus 51 hatnsellceaflhaftgqplp----td~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLP----TDADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCC----CcHHHHHhccccchHHH
Confidence 4677888876666788999998 67888888899998764
No 5
>PLN02417 dihydrodipicolinate synthase
Probab=13.45 E-value=1.2e+02 Score=30.18 Aligned_cols=20 Identities=15% Similarity=0.354 Sum_probs=15.7
Q ss_pred CCCCCCceecCChHHHHHHHH
Q 014260 13 SQVPPGFRFHPTEEELLHYYL 33 (428)
Q Consensus 13 ~~LPpGfRF~PTDeELV~~YL 33 (428)
..+|| |.|.|+++||+.||-
T Consensus 101 ~~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 101 LHINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EEcCC-ccCCCCHHHHHHHHH
Confidence 34566 568999999999873
No 6
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=12.81 E-value=1.8e+02 Score=25.01 Aligned_cols=39 Identities=26% Similarity=0.283 Sum_probs=31.3
Q ss_pred cCChHHHHHHHHHHHhccCCCCCCceeeccCCCCCCchhhhhh
Q 014260 22 HPTEEELLHYYLRKKVAYEKIDLDVIREVDLNKLEPWDIQEKC 64 (428)
Q Consensus 22 ~PTDeELV~~YL~~Kv~g~pl~~~~I~evDVy~~ePWdL~~~~ 64 (428)
|-|.-||++.-...-..|+|+| .+.|+-+..|.+||+..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP----~D~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLP----DDADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCC----ChhhhhhcCcccccHHH
Confidence 5678888876666788999998 56788888899998764
No 7
>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=12.05 E-value=1.4e+02 Score=30.24 Aligned_cols=19 Identities=11% Similarity=0.254 Sum_probs=15.6
Q ss_pred CCCCCCceecCChHHHHHHH
Q 014260 13 SQVPPGFRFHPTEEELLHYY 32 (428)
Q Consensus 13 ~~LPpGfRF~PTDeELV~~Y 32 (428)
+.+|| |.|.|+++||+.||
T Consensus 108 lv~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 108 MLGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred EECCC-cCCCCCHHHHHHHH
Confidence 45677 66999999999987
No 8
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=11.86 E-value=2.2e+02 Score=26.70 Aligned_cols=40 Identities=15% Similarity=0.133 Sum_probs=25.5
Q ss_pred CceecCChHHHHHHHHHHHhccCCCCCCceeeccCC-CCCCchhhhh
Q 014260 18 GFRFHPTEEELLHYYLRKKVAYEKIDLDVIREVDLN-KLEPWDIQEK 63 (428)
Q Consensus 18 GfRF~PTDeELV~~YL~~Kv~g~pl~~~~I~evDVy-~~ePWdL~~~ 63 (428)
|| .+.+-|-+...|+.|+....+| ||+=|+ ++++.|..+=
T Consensus 83 GY--~~~~~~~~L~~L~~R~~~~~FP----HEIGiFLGYPleDV~GF 123 (176)
T PF12672_consen 83 GY--PDSSLEDCLEHLKKRFESGEFP----HEIGIFLGYPLEDVKGF 123 (176)
T ss_pred Cc--CCCCHHHHHHHHHHHhcCCCCC----chhHhccCCCHHHHHHH
Confidence 56 5555554444599888666566 777765 7777666543
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=11.64 E-value=2.5e+02 Score=19.00 Aligned_cols=19 Identities=21% Similarity=0.294 Sum_probs=15.3
Q ss_pred hHHHHHHHHHHHhccCCCC
Q 014260 25 EEELLHYYLRKKVAYEKID 43 (428)
Q Consensus 25 DeELV~~YL~~Kv~g~pl~ 43 (428)
-.|||.+|+.-|+.-+..+
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 4799999999999766544
No 10
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=11.11 E-value=2.1e+02 Score=24.70 Aligned_cols=39 Identities=26% Similarity=0.266 Sum_probs=31.1
Q ss_pred cCChHHHHHHHHHHHhccCCCCCCceeeccCCCCCCchhhhhh
Q 014260 22 HPTEEELLHYYLRKKVAYEKIDLDVIREVDLNKLEPWDIQEKC 64 (428)
Q Consensus 22 ~PTDeELV~~YL~~Kv~g~pl~~~~I~evDVy~~ePWdL~~~~ 64 (428)
|-|.-||++.-...-..|+|+| .+-|+-+..|.+||+..
T Consensus 51 HATNSELLCEAFLHA~TGQPLP----~D~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLP----DDEDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCC----ChhhhhhcCcccchHHH
Confidence 5678888876666788999998 56788888899998654
Done!