Query 019011
Match_columns 347
No_of_seqs 204 out of 990
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:57:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019011.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019011hhsearch_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 8.7E-44 1.9E-48 303.1 6.2 127 14-140 1-129 (129)
2 PHA00692 hypothetical protein 21.5 35 0.00077 26.4 0.3 10 12-21 35-44 (74)
3 smart00265 BH4 BH4 Bcl-2 homol 20.2 1.1E+02 0.0024 20.0 2.4 20 23-42 4-23 (27)
4 PF07960 CBP4: CBP4; InterPro 13.6 95 0.0021 27.4 1.1 11 21-31 30-40 (128)
5 PLN02417 dihydrodipicolinate s 12.3 1.4E+02 0.0031 28.6 2.1 18 14-32 103-120 (280)
6 cd00952 CHBPH_aldolase Trans-o 10.8 1.7E+02 0.0038 28.6 2.1 18 13-31 109-126 (309)
7 PF07131 DUF1382: Protein of u 10.7 1.5E+02 0.0032 23.0 1.2 14 16-29 22-39 (61)
8 PF02180 BH4: Bcl-2 homology r 10.6 2.4E+02 0.0051 18.6 2.0 19 24-42 5-23 (27)
9 cd00490 Met_repressor_MetJ Met 10.4 2E+02 0.0043 24.1 2.0 39 21-63 50-88 (103)
10 smart00707 RPEL Repeat in Dros 10.2 1.6E+02 0.0036 19.0 1.1 13 17-29 6-18 (26)
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=8.7e-44 Score=303.08 Aligned_cols=127 Identities=57% Similarity=1.153 Sum_probs=96.9
Q ss_pred CCCCccccCChHHHHHHHHHHHHcCCCCCC-cceeeccCCCCCCCCCCCcCccCceeEEEEcccCCcCCCCCCCccccCC
Q 019011 14 LPPGFRFYPTDEELLVQYLCRKVAGQHFSL-QIIGEIDLYKFDPWVLPSKAIFGEKEWYFFSPRDRKYPNGSRPNRVAGS 92 (347)
Q Consensus 14 LPPGfRF~PTDEELI~~YL~rKi~g~p~~~-~iI~evDVY~~ePWeLP~~a~~ge~eWYFFs~r~rky~~G~R~nR~tg~ 92 (347)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||.+|||+||.....++++||||+++++++.+|.|.+|++++
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 899999999999999999999999999887 7899999999999999954444667999999999999999999999999
Q ss_pred ceeEeeCcceeEec-CCeEEEEEEEEeeecCCCCCCCccCeEEeeEeec
Q 019011 93 GYWKATGTDKIITT-EGRKVGIKKALVFYVGKAPKGTKTNWIMHEYRLF 140 (347)
Q Consensus 93 GyWK~tG~~k~I~~-~G~~VG~KKtLvFy~gr~pkg~KT~WvMhEYrL~ 140 (347)
|+||.+|+++.|.. +|.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999998876 8999999999999998888999999999999984
No 2
>PHA00692 hypothetical protein
Probab=21.52 E-value=35 Score=26.39 Aligned_cols=10 Identities=60% Similarity=1.305 Sum_probs=8.0
Q ss_pred CCCCCCcccc
Q 019011 12 LNLPPGFRFY 21 (347)
Q Consensus 12 ~~LPPGfRF~ 21 (347)
+..||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4679999995
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=20.20 E-value=1.1e+02 Score=20.00 Aligned_cols=20 Identities=25% Similarity=0.556 Sum_probs=16.1
Q ss_pred ChHHHHHHHHHHHHcCCCCC
Q 019011 23 TDEELLVQYLCRKVAGQHFS 42 (347)
Q Consensus 23 TDEELI~~YL~rKi~g~p~~ 42 (347)
+-.|||.+|+.-|+..+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999876544
No 4
>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=13.63 E-value=95 Score=27.38 Aligned_cols=11 Identities=55% Similarity=0.960 Sum_probs=9.4
Q ss_pred cCChHHHHHHH
Q 019011 21 YPTDEELLVQY 31 (347)
Q Consensus 21 ~PTDEELI~~Y 31 (347)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 59999999865
No 5
>PLN02417 dihydrodipicolinate synthase
Probab=12.29 E-value=1.4e+02 Score=28.63 Aligned_cols=18 Identities=17% Similarity=0.360 Sum_probs=14.2
Q ss_pred CCCCccccCChHHHHHHHH
Q 019011 14 LPPGFRFYPTDEELLVQYL 32 (347)
Q Consensus 14 LPPGfRF~PTDEELI~~YL 32 (347)
+|| +.|.||++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 455 668999999998774
No 6
>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=10.75 E-value=1.7e+02 Score=28.57 Aligned_cols=18 Identities=11% Similarity=0.001 Sum_probs=14.2
Q ss_pred CCCCCccccCChHHHHHHH
Q 019011 13 NLPPGFRFYPTDEELLVQY 31 (347)
Q Consensus 13 ~LPPGfRF~PTDEELI~~Y 31 (347)
-+|| |.|.|+++||+.||
T Consensus 109 v~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 109 LGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred ECCC-cCCCCCHHHHHHHH
Confidence 3555 67899999999876
No 7
>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=10.66 E-value=1.5e+02 Score=23.01 Aligned_cols=14 Identities=57% Similarity=0.897 Sum_probs=11.0
Q ss_pred CCccccC----ChHHHHH
Q 019011 16 PGFRFYP----TDEELLV 29 (347)
Q Consensus 16 PGfRF~P----TDEELI~ 29 (347)
.|+||.| ||+|+..
T Consensus 22 ~GIRFVpiPv~~dee~~~ 39 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHT 39 (61)
T ss_pred cCceeeccccccHHHHHH
Confidence 5999998 7888753
No 8
>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=10.56 E-value=2.4e+02 Score=18.55 Aligned_cols=19 Identities=21% Similarity=0.513 Sum_probs=15.2
Q ss_pred hHHHHHHHHHHHHcCCCCC
Q 019011 24 DEELLVQYLCRKVAGQHFS 42 (347)
Q Consensus 24 DEELI~~YL~rKi~g~p~~ 42 (347)
-.|||.+|+.-|+..+...
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 4799999999998866544
No 9
>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=10.41 E-value=2e+02 Score=24.07 Aligned_cols=39 Identities=28% Similarity=0.292 Sum_probs=31.7
Q ss_pred cCChHHHHHHHHHHHHcCCCCCCcceeeccCCCCCCCCCCCcC
Q 019011 21 YPTDEELLVQYLCRKVAGQHFSLQIIGEIDLYKFDPWVLPSKA 63 (347)
Q Consensus 21 ~PTDEELI~~YL~rKi~g~p~~~~iI~evDVY~~ePWeLP~~a 63 (347)
|-|..||+..-...-..|+|+|.+ .|+-+..|.++|..+
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D----~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDD----ADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCcccccHHH
Confidence 557778887766788899999874 789999999999765
No 10
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=10.20 E-value=1.6e+02 Score=19.03 Aligned_cols=13 Identities=38% Similarity=0.325 Sum_probs=10.5
Q ss_pred CccccCChHHHHH
Q 019011 17 GFRFYPTDEELLV 29 (347)
Q Consensus 17 GfRF~PTDEELI~ 29 (347)
....+||-||||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3467899999996
Done!