Query 030727
Match_columns 172
No_of_seqs 119 out of 907
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 03:41:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030727hhsearch_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-46 2.7E-51 278.6 6.2 125 14-139 1-129 (129)
2 PHA00692 hypothetical protein 52.2 5.7 0.00012 25.4 0.4 11 12-22 35-45 (74)
3 cd00490 Met_repressor_MetJ Met 46.4 25 0.00054 24.3 2.8 37 22-62 51-87 (103)
4 smart00265 BH4 BH4 Bcl-2 homol 43.6 40 0.00086 18.1 2.7 22 22-43 3-24 (27)
5 PRK05264 transcriptional repre 42.1 29 0.00062 24.2 2.6 37 22-62 52-88 (105)
6 PF01340 MetJ: Met Apo-repress 41.5 28 0.00062 24.1 2.5 37 22-62 51-87 (104)
7 PF07960 CBP4: CBP4; InterPro 39.1 17 0.00036 26.9 1.2 12 20-31 29-40 (128)
8 COG3060 MetJ Transcriptional r 34.7 26 0.00057 24.1 1.5 37 22-62 52-88 (105)
9 smart00707 RPEL Repeat in Dros 30.5 37 0.0008 18.0 1.3 13 17-29 6-18 (26)
10 PF02180 BH4: Bcl-2 homology r 30.4 62 0.0013 17.3 2.2 20 23-42 4-23 (27)
11 cd01785 PDZ_GEF_RA Ubiquitin-l 27.1 18 0.00038 24.6 -0.3 24 129-157 29-52 (85)
12 PF13822 ACC_epsilon: Acyl-CoA 26.1 36 0.00078 21.7 1.0 9 21-29 10-18 (62)
13 PLN02417 dihydrodipicolinate s 21.5 62 0.0014 26.6 1.8 20 12-32 101-120 (280)
14 cd00954 NAL N-Acetylneuraminic 20.2 68 0.0015 26.4 1.8 19 13-32 102-120 (288)
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-46 Score=278.57 Aligned_cols=125 Identities=57% Similarity=1.143 Sum_probs=95.1
Q ss_pred CCCCeEECCChHHHHHHHHHHhHhCCCCCC-cceeccCCCCCCCCCCCc---CCCcceEEeecccccCCCCCCCcccCCc
Q 030727 14 LPPGFRFHPTDEELVVQYLKRKIFACPLPA-SIIPEVDVCKSDPWDLPG---DVAQERYFFSTREAKYPNGNRSNRATGS 89 (172)
Q Consensus 14 lp~G~rF~PTDeELi~~yL~~k~~g~~lp~-~~I~~~Dvy~~~P~~Lp~---~~~~~~yFF~~~~~~~~~g~r~~R~~~~ 89 (172)
|||||||+|||+|||.+||++|+.|.++|. ++|+++|||++|||+|+. ..+++||||+++++++.++.|.+|++++
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 799999999999999993 3357999999999999999999999999
Q ss_pred ceeeeeCCCceEEeCCCCeeeEEEEEEEeecCCCCCCCCcCeEEEEEEeC
Q 030727 90 GYWKATGLDKQIATSRGNQIVGMKKTLVFYRGKPPHGSRTDWIMHEYRLV 139 (172)
Q Consensus 90 G~Wk~~g~~k~i~~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~l~ 139 (172)
|+||++|+.++|.+. +|.+||+|++|+|+.++.+++.+|+|+||||+|.
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 999999999999874 8899999999999988778889999999999984
No 2
>PHA00692 hypothetical protein
Probab=52.22 E-value=5.7 Score=25.36 Aligned_cols=11 Identities=55% Similarity=1.201 Sum_probs=8.9
Q ss_pred cCCCCCeEECC
Q 030727 12 LRLPPGFRFHP 22 (172)
Q Consensus 12 ~~lp~G~rF~P 22 (172)
...||||||--
T Consensus 35 veyppgfrfgg 45 (74)
T PHA00692 35 VEYPPGFRFGG 45 (74)
T ss_pred EecCCCccccc
Confidence 56899999953
No 3
>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=46.43 E-value=25 Score=24.33 Aligned_cols=37 Identities=24% Similarity=0.428 Sum_probs=28.0
Q ss_pred CChHHHHHHHHHHhHhCCCCCCcceeccCCCCCCCCCCCcC
Q 030727 22 PTDEELVVQYLKRKIFACPLPASIIPEVDVCKSDPWDLPGD 62 (172)
Q Consensus 22 PTDeELi~~yL~~k~~g~~lp~~~I~~~Dvy~~~P~~Lp~~ 62 (172)
-|..||+..-...-..|+|||. +.|+-...|.++|..
T Consensus 51 ATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 51 ATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEA 87 (103)
T ss_pred cccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHH
Confidence 4667777754455578999998 578888889888864
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=43.55 E-value=40 Score=18.06 Aligned_cols=22 Identities=27% Similarity=0.289 Sum_probs=16.6
Q ss_pred CChHHHHHHHHHHhHhCCCCCC
Q 030727 22 PTDEELVVQYLKRKIFACPLPA 43 (172)
Q Consensus 22 PTDeELi~~yL~~k~~g~~lp~ 43 (172)
.+-.|||.+|+.-|+.-...+.
T Consensus 3 ~~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 3 LDNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred cchHHHHHHHHHHHHhhcCCCC
Confidence 3557999999999997654443
No 5
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=42.10 E-value=29 Score=24.19 Aligned_cols=37 Identities=24% Similarity=0.410 Sum_probs=27.8
Q ss_pred CChHHHHHHHHHHhHhCCCCCCcceeccCCCCCCCCCCCcC
Q 030727 22 PTDEELVVQYLKRKIFACPLPASIIPEVDVCKSDPWDLPGD 62 (172)
Q Consensus 22 PTDeELi~~yL~~k~~g~~lp~~~I~~~Dvy~~~P~~Lp~~ 62 (172)
-|..||+.--...-..|+|||. +.|+-...|.++|..
T Consensus 52 ATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~ 88 (105)
T PRK05264 52 ATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEA 88 (105)
T ss_pred cccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHH
Confidence 4667877754445578999998 578888888888854
No 6
>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=41.45 E-value=28 Score=24.11 Aligned_cols=37 Identities=27% Similarity=0.515 Sum_probs=21.2
Q ss_pred CChHHHHHHHHHHhHhCCCCCCcceeccCCCCCCCCCCCcC
Q 030727 22 PTDEELVVQYLKRKIFACPLPASIIPEVDVCKSDPWDLPGD 62 (172)
Q Consensus 22 PTDeELi~~yL~~k~~g~~lp~~~I~~~Dvy~~~P~~Lp~~ 62 (172)
-|..||+..-...-..|+|||. +.|+-...|..+|..
T Consensus 51 ATNSeLLcEAFLHAfTGQPLP~----D~dl~kd~~d~ip~~ 87 (104)
T PF01340_consen 51 ATNSELLCEAFLHAFTGQPLPT----DDDLRKDRPDEIPAE 87 (104)
T ss_dssp -SHHHHHHHHHHHHHH----------TTGGGSTSGSSS-HH
T ss_pred cccHHHHHHHHHHHhcCCCCCC----hhhhhhcCCccchHH
Confidence 4777887754455578999998 578888889888854
No 7
>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=39.08 E-value=17 Score=26.91 Aligned_cols=12 Identities=50% Similarity=0.811 Sum_probs=9.9
Q ss_pred ECCChHHHHHHH
Q 030727 20 FHPTDEELVVQY 31 (172)
Q Consensus 20 F~PTDeELi~~y 31 (172)
=.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 379999999764
No 8
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=34.69 E-value=26 Score=24.07 Aligned_cols=37 Identities=24% Similarity=0.436 Sum_probs=27.4
Q ss_pred CChHHHHHHHHHHhHhCCCCCCcceeccCCCCCCCCCCCcC
Q 030727 22 PTDEELVVQYLKRKIFACPLPASIIPEVDVCKSDPWDLPGD 62 (172)
Q Consensus 22 PTDeELi~~yL~~k~~g~~lp~~~I~~~Dvy~~~P~~Lp~~ 62 (172)
-|..||+..-...-..|+|||. +.|+...-|.++|..
T Consensus 52 atnsellceaflhaftgqplpt----d~dl~ker~deipe~ 88 (105)
T COG3060 52 ATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEA 88 (105)
T ss_pred hhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHH
Confidence 4667777654555578999997 578888888888864
No 9
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=30.52 E-value=37 Score=18.00 Aligned_cols=13 Identities=38% Similarity=0.409 Sum_probs=10.7
Q ss_pred CeEECCChHHHHH
Q 030727 17 GFRFHPTDEELVV 29 (172)
Q Consensus 17 G~rF~PTDeELi~ 29 (172)
...++|+-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3468999999996
No 10
>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=30.39 E-value=62 Score=17.32 Aligned_cols=20 Identities=25% Similarity=0.316 Sum_probs=15.2
Q ss_pred ChHHHHHHHHHHhHhCCCCC
Q 030727 23 TDEELVVQYLKRKIFACPLP 42 (172)
Q Consensus 23 TDeELi~~yL~~k~~g~~lp 42 (172)
.-.|||.+|+.-|+.-..++
T Consensus 4 ~nR~lV~~yi~yKLsQrgy~ 23 (27)
T PF02180_consen 4 DNRELVEDYISYKLSQRGYV 23 (27)
T ss_dssp HHHHHHHHHHHHHHHHTTST
T ss_pred cHHHHHHHHHHHHhhhcCCC
Confidence 34799999999999755444
No 11
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=27.12 E-value=18 Score=24.61 Aligned_cols=24 Identities=13% Similarity=0.329 Sum_probs=19.0
Q ss_pred cCeEEEEEEeCCCCCCCCCCCeeEEEEEE
Q 030727 129 TDWIMHEYRLVTAANAPQKKNLPSCGNGQ 157 (172)
Q Consensus 129 t~W~M~EY~l~~~~~~~~~~~~VLCkv~~ 157 (172)
+.-.|+||.+...+ .+|.||.|--
T Consensus 29 v~lal~eFgi~~~s-----~~~sLceVtV 52 (85)
T cd01785 29 VMLALQEFGITAPS-----SNFSLCEVSV 52 (85)
T ss_pred HHHHHHHhCCCCCc-----cceEEEEEEe
Confidence 45678999999875 5999999764
No 12
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=26.13 E-value=36 Score=21.66 Aligned_cols=9 Identities=67% Similarity=1.014 Sum_probs=7.8
Q ss_pred CCChHHHHH
Q 030727 21 HPTDEELVV 29 (172)
Q Consensus 21 ~PTDeELi~ 29 (172)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999975
No 13
>PLN02417 dihydrodipicolinate synthase
Probab=21.50 E-value=62 Score=26.58 Aligned_cols=20 Identities=20% Similarity=0.451 Sum_probs=15.1
Q ss_pred cCCCCCeEECCChHHHHHHHH
Q 030727 12 LRLPPGFRFHPTDEELVVQYL 32 (172)
Q Consensus 12 ~~lp~G~rF~PTDeELi~~yL 32 (172)
+-+|| +.|.||+++|+.||-
T Consensus 101 ~~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 101 LHINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EEcCC-ccCCCCHHHHHHHHH
Confidence 34566 558999999998763
No 14
>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=20.22 E-value=68 Score=26.40 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=13.7
Q ss_pred CCCCCeEECCChHHHHHHHH
Q 030727 13 RLPPGFRFHPTDEELVVQYL 32 (172)
Q Consensus 13 ~lp~G~rF~PTDeELi~~yL 32 (172)
-+||-| |.||++||+.||.
T Consensus 102 ~~~P~y-~~~~~~~i~~~~~ 120 (288)
T cd00954 102 AITPFY-YKFSFEEIKDYYR 120 (288)
T ss_pred EeCCCC-CCCCHHHHHHHHH
Confidence 346644 7899999997653
Done!