Query 015924
Match_columns 398
No_of_seqs 189 out of 987
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 02:10:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015924.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015924hhsearch_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 5E-43 1.1E-47 302.9 6.2 128 14-142 1-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 39.8 32 0.0007 23.2 2.5 21 23-43 4-24 (27)
3 PF02180 BH4: Bcl-2 homology r 22.5 82 0.0018 21.3 2.1 21 23-43 4-24 (27)
4 cd00490 Met_repressor_MetJ Met 15.2 1.5E+02 0.0033 25.4 2.7 38 21-62 50-87 (103)
5 PF01340 MetJ: Met Apo-repress 13.8 1.7E+02 0.0037 25.2 2.6 38 21-62 50-87 (104)
6 PRK05264 transcriptional repre 13.8 1.7E+02 0.0036 25.4 2.6 37 21-61 51-87 (105)
7 PF09174 Maf1: Maf1 regulator; 13.8 64 0.0014 30.1 0.1 12 46-57 137-148 (179)
8 COG3060 MetJ Transcriptional r 13.2 1.1E+02 0.0025 26.0 1.4 38 21-62 51-88 (105)
9 KOG1334 WD40 repeat protein [G 12.7 3.7E+02 0.008 29.6 5.3 91 25-118 303-425 (559)
10 PF07960 CBP4: CBP4; InterPro 12.1 1.1E+02 0.0024 27.6 1.1 16 21-36 30-48 (128)
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=5e-43 Score=302.95 Aligned_cols=128 Identities=55% Similarity=1.141 Sum_probs=97.2
Q ss_pred CCCCceeCCChHHHHHHHHHHHHhCCCCCc-CceeeccCCCCCCCCCcccccCCCceEEEEecccccccCCCCCceeccc
Q 015924 14 MLPGFRFHPTDEELVGFYLKRKIQHRPLPI-ELIKQVDIYKYDPWDLPKLATAGEKEWYFYCPRDRKYRNSARPNRVTGA 92 (398)
Q Consensus 14 LPPGfRF~PTDEELV~~YL~rKi~g~pLp~-~~I~evDVY~~ePwdLP~~~~~ge~eWYFFspr~rK~~~G~R~nR~tgg 92 (398)
|||||||+|||||||.+||++|+.|.+++. .+|+++|||++|||+||+....++++||||+++++++.++.|.+|++++
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 899999999999999999999999999888 7999999999999999964445677999999999999999999999999
Q ss_pred ceeeccCCCccEEcCCCCeEEEEEEEEEEeecCCCCCCccCceEeeeecC
Q 015924 93 GFWKATGTDRPIYSSDGTKCIGLKKSLVFYRGRAAKGIKTDWMMHEFRLP 142 (398)
Q Consensus 93 GyWK~tG~~k~I~~~~G~~vIG~KKtLvFY~Grap~g~KT~WvMhEYrL~ 142 (398)
|+||++|+.++|.+. ++++||+||+|+||.++.+++.||+|+||||+|.
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 4589999999999998888999999999999983
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=39.84 E-value=32 Score=23.19 Aligned_cols=21 Identities=24% Similarity=0.279 Sum_probs=17.3
Q ss_pred ChHHHHHHHHHHHHhCCCCCc
Q 015924 23 TDEELVGFYLKRKIQHRPLPI 43 (398)
Q Consensus 23 TDEELV~~YL~rKi~g~pLp~ 43 (398)
+-.|||.+|+.-|+..+..++
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCC
Confidence 467999999999998776654
No 3
>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=22.52 E-value=82 Score=21.31 Aligned_cols=21 Identities=29% Similarity=0.384 Sum_probs=16.9
Q ss_pred ChHHHHHHHHHHHHhCCCCCc
Q 015924 23 TDEELVGFYLKRKIQHRPLPI 43 (398)
Q Consensus 23 TDEELV~~YL~rKi~g~pLp~ 43 (398)
.-.|||.+|+.-|+..+..++
T Consensus 4 ~nR~lV~~yi~yKLsQrgy~w 24 (27)
T PF02180_consen 4 DNRELVEDYISYKLSQRGYVW 24 (27)
T ss_dssp HHHHHHHHHHHHHHHHTTSTS
T ss_pred cHHHHHHHHHHHHhhhcCCCC
Confidence 347999999999997776654
No 4
>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=15.24 E-value=1.5e+02 Score=25.41 Aligned_cols=38 Identities=26% Similarity=0.390 Sum_probs=31.6
Q ss_pred CCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCccc
Q 015924 21 HPTDEELVGFYLKRKIQHRPLPIELIKQVDIYKYDPWDLPKL 62 (398)
Q Consensus 21 ~PTDEELV~~YL~rKi~g~pLp~~~I~evDVY~~ePwdLP~~ 62 (398)
|-|.-||+..-...-..|+|||. +.|+-+..|.++|+.
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHH
Confidence 56778888877777889999997 678999999999873
No 5
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=13.83 E-value=1.7e+02 Score=25.19 Aligned_cols=38 Identities=29% Similarity=0.426 Sum_probs=24.7
Q ss_pred CCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCccc
Q 015924 21 HPTDEELVGFYLKRKIQHRPLPIELIKQVDIYKYDPWDLPKL 62 (398)
Q Consensus 21 ~PTDEELV~~YL~rKi~g~pLp~~~I~evDVY~~ePwdLP~~ 62 (398)
|-|.-||+..-...-..|+|||. +.|+-+..|.++|..
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~----D~dl~kd~~d~ip~~ 87 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT----DDDLRKDRPDEIPAE 87 (104)
T ss_dssp S-SHHHHHHHHHHHHHH----------TTGGGSTSGSSS-HH
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCCccchHH
Confidence 56888888877777889999997 678999999999873
No 6
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=13.78 E-value=1.7e+02 Score=25.36 Aligned_cols=37 Identities=27% Similarity=0.393 Sum_probs=31.2
Q ss_pred CCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCcc
Q 015924 21 HPTDEELVGFYLKRKIQHRPLPIELIKQVDIYKYDPWDLPK 61 (398)
Q Consensus 21 ~PTDEELV~~YL~rKi~g~pLp~~~I~evDVY~~ePwdLP~ 61 (398)
|-|.-||+..-...-..|+|||. +-|+-+..|.++|+
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~ 87 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPE 87 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchH
Confidence 56778888877777889999997 67899999999996
No 7
>PF09174 Maf1: Maf1 regulator; InterPro: IPR015257 Maf1 is a negative regulator of RNA polymerase III [, ]. It targets the initiation factor TFIIIB []. ; PDB: 3NR5_A.
Probab=13.77 E-value=64 Score=30.13 Aligned_cols=12 Identities=50% Similarity=0.997 Sum_probs=6.7
Q ss_pred eeeccCCCCCCC
Q 015924 46 IKQVDIYKYDPW 57 (398)
Q Consensus 46 I~evDVY~~ePw 57 (398)
+.++|||.+.|.
T Consensus 137 l~~C~iYsy~pd 148 (179)
T PF09174_consen 137 LKDCDIYSYNPD 148 (179)
T ss_dssp GGG-EEEEE---
T ss_pred ccCceEEEEccC
Confidence 458899999994
No 8
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=13.17 E-value=1.1e+02 Score=26.02 Aligned_cols=38 Identities=26% Similarity=0.418 Sum_probs=31.2
Q ss_pred CCChHHHHHHHHHHHHhCCCCCcCceeeccCCCCCCCCCccc
Q 015924 21 HPTDEELVGFYLKRKIQHRPLPIELIKQVDIYKYDPWDLPKL 62 (398)
Q Consensus 21 ~PTDEELV~~YL~rKi~g~pLp~~~I~evDVY~~ePwdLP~~ 62 (398)
|-|..||+..-...-..|+|||. +.|+.+.-|.++|+.
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~ 88 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEA 88 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHH
Confidence 56778888877777789999986 679999999999874
No 9
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=12.70 E-value=3.7e+02 Score=29.64 Aligned_cols=91 Identities=18% Similarity=0.247 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHhCCCCCc---Cceeecc-----------CCCCCCCCCcccccCCCceEEEEecccccc----------
Q 015924 25 EELVGFYLKRKIQHRPLPI---ELIKQVD-----------IYKYDPWDLPKLATAGEKEWYFYCPRDRKY---------- 80 (398)
Q Consensus 25 EELV~~YL~rKi~g~pLp~---~~I~evD-----------VY~~ePwdLP~~~~~ge~eWYFFspr~rK~---------- 80 (398)
+|.+.-|=.|++...+..- .+-+..+ +|.+++-+|.+ .+.+...|||.+-....
T Consensus 303 dqf~RvYD~R~~~~e~~n~~~~~f~p~hl~~d~~v~ITgl~Ysh~~sElLa--SYnDe~IYLF~~~~~~G~~p~~~s~~~ 380 (559)
T KOG1334|consen 303 DQFARVYDQRRIDKEENNGVLDKFCPHHLVEDDPVNITGLVYSHDGSELLA--SYNDEDIYLFNKSMGDGSEPDPSSPRE 380 (559)
T ss_pred hhhhhhhcccchhhccccchhhhcCCccccccCcccceeEEecCCccceee--eecccceEEeccccccCCCCCCCcchh
Confidence 4566667888887653221 1222222 56666666643 34456678885432111
Q ss_pred ------cCCCCCceec-ccceeeccCCCccEEcCCCCeE-EEEEEE
Q 015924 81 ------RNSARPNRVT-GAGFWKATGTDRPIYSSDGTKC-IGLKKS 118 (398)
Q Consensus 81 ------~~G~R~nR~t-ggGyWK~tG~~k~I~~~~G~~v-IG~KKt 118 (398)
=.|+|-+|+. |.-+|-+.. +-.|-..+.|.+ |+.|++
T Consensus 381 ~~~k~vYKGHrN~~TVKgVNFfGPrs-EyVvSGSDCGhIFiW~K~t 425 (559)
T KOG1334|consen 381 QYVKRVYKGHRNSRTVKGVNFFGPRS-EYVVSGSDCGHIFIWDKKT 425 (559)
T ss_pred hccchhhcccccccccceeeeccCcc-ceEEecCccceEEEEecch
Confidence 1255666654 446774432 233333444554 666654
No 10
>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=12.15 E-value=1.1e+02 Score=27.63 Aligned_cols=16 Identities=44% Similarity=0.806 Sum_probs=12.5
Q ss_pred CCChHHHHHHH---HHHHH
Q 015924 21 HPTDEELVGFY---LKRKI 36 (398)
Q Consensus 21 ~PTDEELV~~Y---L~rKi 36 (398)
.||||||+..| |+++.
T Consensus 30 tPTeEeL~~r~sPELrkr~ 48 (128)
T PF07960_consen 30 TPTEEELFKRYSPELRKRY 48 (128)
T ss_pred CCCHHHHHHhcCHHHHHHH
Confidence 49999999987 55554
Done!