Query 018596
Match_columns 353
No_of_seqs 229 out of 1015
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 02:25:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018596.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018596hhsearch_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 4E-43 8.7E-48 299.8 7.3 127 7-136 1-129 (129)
2 PHA00692 hypothetical protein 38.0 11 0.00025 29.1 0.1 11 4-14 34-44 (74)
3 PF07960 CBP4: CBP4; InterPro 21.2 65 0.0014 28.4 1.9 17 14-30 30-49 (128)
4 smart00265 BH4 BH4 Bcl-2 homol 17.8 1.5E+02 0.0032 19.5 2.5 20 16-35 4-23 (27)
5 PF04700 Baculo_gp41: Structur 15.6 1.4E+02 0.003 28.0 2.8 17 16-32 6-24 (186)
6 KOG3238 Chloride ion current i 12.6 2.6E+02 0.0056 26.7 3.7 61 9-70 111-171 (216)
7 PLN02417 dihydrodipicolinate s 12.5 1E+02 0.0022 29.7 1.1 22 4-26 100-121 (280)
8 cd00952 CHBPH_aldolase Trans-o 11.9 1.4E+02 0.003 29.3 1.9 20 4-24 107-126 (309)
9 TIGR02313 HpaI-NOT-DapA 2,4-di 11.6 1.2E+02 0.0026 29.6 1.2 22 4-26 99-120 (294)
10 PF01473 CW_binding_1: Putativ 11.6 1.6E+02 0.0034 17.0 1.3 8 63-70 7-14 (19)
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=4e-43 Score=299.83 Aligned_cols=127 Identities=54% Similarity=1.101 Sum_probs=96.5
Q ss_pred CCCCceECCChHHHHHHHHHHHHhCCCCCC-CceeeccCCCCCCCchhhhhhcCCCCCceEEEEecCCCCCCCCCccccc
Q 018596 7 VPPGFRFHPTDEELVDYYLRKKITSRRIDL-DVIKDVDLYKIEPWDLQELCRIGTEEQNEWYFFSHKDKKYPTGTRTNRA 85 (353)
Q Consensus 7 LPPGfRF~PTDeELV~~YLr~Kv~g~~l~~-~vI~evDVY~~ePWdL~~~~~~g~~~~~eWYFFs~r~kK~~~G~R~nRa 85 (353)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||+.|||+|+.... ..+.+||||+++.+++++|.|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~---~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFK---GGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSS---S-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhcc---CCCceEEEEEecccccCCccccccc
Confidence 899999999999999999999999999887 799999999999999995222 2346999999999999999999999
Q ss_pred ccCCeeeecCCCceeec-CCeeEEEEEEEEEeecCCCCCCCcCeEEEEEEeC
Q 018596 86 TTAGFWKATGRDKAIYS-KHDLIGMRKTLVFYKGRAPNGQKSDWIMHEYRLE 136 (353)
Q Consensus 86 tg~G~WK~tG~~k~I~~-~g~~IG~KKtLvFy~gr~p~g~KT~WiMhEYrL~ 136 (353)
+++|+||.+|++++|.+ ++.+||+|++|+||.++.+++.+|+|+||||+|+
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 99999999999999998 8899999999999999888999999999999984
No 2
>PHA00692 hypothetical protein
Probab=38.00 E-value=11 Score=29.08 Aligned_cols=11 Identities=64% Similarity=1.343 Sum_probs=8.8
Q ss_pred CCCCCCCceEC
Q 018596 4 FSHVPPGFRFH 14 (353)
Q Consensus 4 ~s~LPPGfRF~ 14 (353)
+...||||||-
T Consensus 34 fveyppgfrfg 44 (74)
T PHA00692 34 FVEYPPGFRFG 44 (74)
T ss_pred eEecCCCcccc
Confidence 45789999995
No 3
>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=21.19 E-value=65 Score=28.42 Aligned_cols=17 Identities=53% Similarity=0.841 Sum_probs=13.1
Q ss_pred CCChHHHHHHH---HHHHHh
Q 018596 14 HPTDEELVDYY---LRKKIT 30 (353)
Q Consensus 14 ~PTDeELV~~Y---Lr~Kv~ 30 (353)
.||||||+..| |+++..
T Consensus 30 tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 30 TPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred CCCHHHHHHhcCHHHHHHHH
Confidence 49999999987 665553
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=17.79 E-value=1.5e+02 Score=19.48 Aligned_cols=20 Identities=25% Similarity=0.404 Sum_probs=15.5
Q ss_pred ChHHHHHHHHHHHHhCCCCC
Q 018596 16 TDEELVDYYLRKKITSRRID 35 (353)
Q Consensus 16 TDeELV~~YLr~Kv~g~~l~ 35 (353)
+-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999998655443
No 5
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=15.61 E-value=1.4e+02 Score=27.99 Aligned_cols=17 Identities=53% Similarity=0.940 Sum_probs=9.5
Q ss_pred ChHHHHHHH--HHHHHhCC
Q 018596 16 TDEELVDYY--LRKKITSR 32 (353)
Q Consensus 16 TDeELV~~Y--Lr~Kv~g~ 32 (353)
+|||||.|| |.+|..|.
T Consensus 6 sDe~Li~yY~~L~K~~g~~ 24 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGS 24 (186)
T ss_pred cHHHHHHHHHHHHHHhCCC
Confidence 567777766 33444433
No 6
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=12.58 E-value=2.6e+02 Score=26.67 Aligned_cols=61 Identities=21% Similarity=0.401 Sum_probs=34.8
Q ss_pred CCceECCChHHHHHHHHHHHHhCCCCCCCceeeccCCCCCCCchhhhhhcCCCCCceEEEEe
Q 018596 9 PGFRFHPTDEELVDYYLRKKITSRRIDLDVIKDVDLYKIEPWDLQELCRIGTEEQNEWYFFS 70 (353)
Q Consensus 9 PGfRF~PTDeELV~~YLr~Kv~g~~l~~~vI~evDVY~~ePWdL~~~~~~g~~~~~eWYFFs 70 (353)
-+|||+|+|.--+.-.---..-...+-+....+.+-|.-+=|+...- ..|.+....||=+.
T Consensus 111 ~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~-d~~~gDs~~~~t~d 171 (216)
T KOG3238|consen 111 TEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAH-DAGQGDSPNSYTYD 171 (216)
T ss_pred ccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhh-hccCCCCccccccc
Confidence 48999999987766533323333333333366777777777776543 33433334555443
No 7
>PLN02417 dihydrodipicolinate synthase
Probab=12.46 E-value=1e+02 Score=29.72 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=16.5
Q ss_pred CCCCCCCceECCChHHHHHHHHH
Q 018596 4 FSHVPPGFRFHPTDEELVDYYLR 26 (353)
Q Consensus 4 ~s~LPPGfRF~PTDeELV~~YLr 26 (353)
+.-+|| +.|.||++||+.||-.
T Consensus 100 v~~~~P-~y~~~~~~~i~~~f~~ 121 (280)
T PLN02417 100 ALHINP-YYGKTSQEGLIKHFET 121 (280)
T ss_pred EEEcCC-ccCCCCHHHHHHHHHH
Confidence 344677 5589999999998743
No 8
>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=11.90 E-value=1.4e+02 Score=29.33 Aligned_cols=20 Identities=15% Similarity=0.205 Sum_probs=15.9
Q ss_pred CCCCCCCceECCChHHHHHHH
Q 018596 4 FSHVPPGFRFHPTDEELVDYY 24 (353)
Q Consensus 4 ~s~LPPGfRF~PTDeELV~~Y 24 (353)
+.-+|| |.|.|+++||+.||
T Consensus 107 vlv~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 107 TMLGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred EEECCC-cCCCCCHHHHHHHH
Confidence 344677 56899999999987
No 9
>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=11.64 E-value=1.2e+02 Score=29.58 Aligned_cols=22 Identities=23% Similarity=0.366 Sum_probs=16.6
Q ss_pred CCCCCCCceECCChHHHHHHHHH
Q 018596 4 FSHVPPGFRFHPTDEELVDYYLR 26 (353)
Q Consensus 4 ~s~LPPGfRF~PTDeELV~~YLr 26 (353)
+.-+||-| |.|++++|+.||-.
T Consensus 99 v~v~pP~y-~~~~~~~l~~~f~~ 120 (294)
T TIGR02313 99 AMVIVPYY-NKPNQEALYDHFAE 120 (294)
T ss_pred EEEcCccC-CCCCHHHHHHHHHH
Confidence 34466665 89999999998743
No 10
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=11.62 E-value=1.6e+02 Score=16.96 Aligned_cols=8 Identities=38% Similarity=1.522 Sum_probs=6.2
Q ss_pred CceEEEEe
Q 018596 63 QNEWYFFS 70 (353)
Q Consensus 63 ~~eWYFFs 70 (353)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 36899995
Done!