Query 039532
Match_columns 268
No_of_seqs 148 out of 952
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 10:38:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039532.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039532hhsearch_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 2.2E-43 4.8E-48 288.7 6.4 129 5-141 1-129 (129)
2 PHA00692 hypothetical protein 35.7 15 0.00032 26.4 0.4 9 4-12 36-44 (74)
3 smart00265 BH4 BH4 Bcl-2 homol 32.0 41 0.00088 20.4 1.8 19 14-32 4-22 (27)
4 PF07960 CBP4: CBP4; InterPro 21.8 48 0.001 27.4 1.1 11 12-22 30-40 (128)
5 PF02180 BH4: Bcl-2 homology r 21.4 90 0.0019 18.9 2.0 18 15-32 5-22 (27)
6 PLN02417 dihydrodipicolinate s 14.9 1.1E+02 0.0023 28.0 2.0 18 5-23 103-120 (280)
7 PF07131 DUF1382: Protein of u 14.8 1.2E+02 0.0025 21.9 1.6 14 7-20 22-39 (61)
8 TIGR02313 HpaI-NOT-DapA 2,4-di 14.3 1.2E+02 0.0025 28.0 2.0 18 5-23 102-119 (294)
9 cd00954 NAL N-Acetylneuraminic 13.8 1.2E+02 0.0025 27.8 1.9 19 5-24 103-121 (288)
10 smart00707 RPEL Repeat in Dros 13.2 1.3E+02 0.0029 18.0 1.3 13 8-20 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=2.2e-43 Score=288.68 Aligned_cols=129 Identities=44% Similarity=0.953 Sum_probs=95.5
Q ss_pred CCCCceeCCChHHHHHHHHHHHHcCCCCCcccccCcceeecCCCCCCCCCcccchhcccCCCCceEEEeecCcccccCCC
Q 039532 5 YPPGFRFYPTEEELVSFYLHNKLAGHRQDLNLQMDRIIPVINIYDYNPWDLPQFSQLLCHRDPEQWFFFIPRQESEARGG 84 (268)
Q Consensus 5 LPpGfRF~PTDeELV~~YL~~Ki~g~~~~l~~~~~~~I~~~DVy~~~Pw~Lp~~~~~~~~gd~~~wyFFt~r~~k~~~G~ 84 (268)
|||||||+|||+|||.+||++|+.|++++ ...+|+++|||++|||+|+.. . .+.+++||||++++++..+|.
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~----~~~~i~~~Diy~~~P~~L~~~---~-~~~~~~~yFF~~~~~~~~~~~ 72 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLP----CEDVIHDVDIYSAHPWELPAK---F-KGGDEEWYFFSPRKKKYPNGG 72 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHC----S-CHSEE--GGGS-GGGCHHH---S-SS-SSEEEEEEE---------
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCC----cccceeecccCccChHHhhhh---c-cCCCceEEEEEecccccCCcc
Confidence 89999999999999999999999999987 568899999999999999952 1 123447999999999988999
Q ss_pred CCccccccceeeecCCCceeecCCCceEEEEEEEEEeecCCCCCCCcCcEEEEEEeC
Q 039532 85 RPNRLTSAGYWKATGSPGLVYSSNNRPVGEKRTMVFYRGRAPNGRKTEWKMNEYKAI 141 (268)
Q Consensus 85 R~~R~t~~G~Wk~~G~~k~V~~~~g~viG~Krtf~Fy~g~~p~g~kT~W~M~EY~l~ 141 (268)
|++|++++|+||.+|+.+.|.+.+|.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 73 r~~R~~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 73 RPNRVTGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp -S-EEETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cccccccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999999999999877999999999999998888889999999999984
No 2
>PHA00692 hypothetical protein
Probab=35.69 E-value=15 Score=26.38 Aligned_cols=9 Identities=78% Similarity=1.737 Sum_probs=7.6
Q ss_pred CCCCCceeC
Q 039532 4 DYPPGFRFY 12 (268)
Q Consensus 4 ~LPpGfRF~ 12 (268)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 479999995
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=32.00 E-value=41 Score=20.36 Aligned_cols=19 Identities=32% Similarity=0.361 Sum_probs=15.3
Q ss_pred ChHHHHHHHHHHHHcCCCC
Q 039532 14 TEEELVSFYLHNKLAGHRQ 32 (268)
Q Consensus 14 TDeELV~~YL~~Ki~g~~~ 32 (268)
+-.|||.+|+.-||.-+..
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999975544
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=21.84 E-value=48 Score=27.42 Aligned_cols=11 Identities=64% Similarity=0.842 Sum_probs=9.3
Q ss_pred CCChHHHHHHH
Q 039532 12 YPTEEELVSFY 22 (268)
Q Consensus 12 ~PTDeELV~~Y 22 (268)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999764
No 5
>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=21.41 E-value=90 Score=18.90 Aligned_cols=18 Identities=33% Similarity=0.412 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHHHcCCCC
Q 039532 15 EEELVSFYLHNKLAGHRQ 32 (268)
Q Consensus 15 DeELV~~YL~~Ki~g~~~ 32 (268)
-.|||.+|+.-||.-+..
T Consensus 5 nR~lV~~yi~yKLsQrgy 22 (27)
T PF02180_consen 5 NRELVEDYISYKLSQRGY 22 (27)
T ss_dssp HHHHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHHhhhcCC
Confidence 479999999999965443
No 6
>PLN02417 dihydrodipicolinate synthase
Probab=14.94 E-value=1.1e+02 Score=28.00 Aligned_cols=18 Identities=17% Similarity=0.325 Sum_probs=14.2
Q ss_pred CCCCceeCCChHHHHHHHH
Q 039532 5 YPPGFRFYPTEEELVSFYL 23 (268)
Q Consensus 5 LPpGfRF~PTDeELV~~YL 23 (268)
+|| |-|.||++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 456 458899999999874
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=14.82 E-value=1.2e+02 Score=21.88 Aligned_cols=14 Identities=50% Similarity=0.883 Sum_probs=10.7
Q ss_pred CCceeCC----ChHHHHH
Q 039532 7 PGFRFYP----TEEELVS 20 (268)
Q Consensus 7 pGfRF~P----TDeELV~ 20 (268)
.|+||.| ||+|+..
T Consensus 22 ~GIRFVpiPv~~dee~~~ 39 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHT 39 (61)
T ss_pred cCceeeccccccHHHHHH
Confidence 4999998 7777653
No 8
>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=14.28 E-value=1.2e+02 Score=28.03 Aligned_cols=18 Identities=22% Similarity=0.401 Sum_probs=14.0
Q ss_pred CCCCceeCCChHHHHHHHH
Q 039532 5 YPPGFRFYPTEEELVSFYL 23 (268)
Q Consensus 5 LPpGfRF~PTDeELV~~YL 23 (268)
+||-| |.|++++|+.||-
T Consensus 102 ~pP~y-~~~~~~~l~~~f~ 119 (294)
T TIGR02313 102 IVPYY-NKPNQEALYDHFA 119 (294)
T ss_pred cCccC-CCCCHHHHHHHHH
Confidence 45555 8899999999863
No 9
>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=13.85 E-value=1.2e+02 Score=27.78 Aligned_cols=19 Identities=21% Similarity=0.415 Sum_probs=13.9
Q ss_pred CCCCceeCCChHHHHHHHHH
Q 039532 5 YPPGFRFYPTEEELVSFYLH 24 (268)
Q Consensus 5 LPpGfRF~PTDeELV~~YL~ 24 (268)
+||-| |.||++||+.||..
T Consensus 103 ~~P~y-~~~~~~~i~~~~~~ 121 (288)
T cd00954 103 ITPFY-YKFSFEEIKDYYRE 121 (288)
T ss_pred eCCCC-CCCCHHHHHHHHHH
Confidence 35544 77999999997643
No 10
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=13.24 E-value=1.3e+02 Score=17.97 Aligned_cols=13 Identities=38% Similarity=0.419 Sum_probs=10.7
Q ss_pred CceeCCChHHHHH
Q 039532 8 GFRFYPTEEELVS 20 (268)
Q Consensus 8 GfRF~PTDeELV~ 20 (268)
...++|+-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4567899999997
Done!