Query 045278
Match_columns 221
No_of_seqs 178 out of 913
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 11:38:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045278.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045278hhsearch_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-45 1.1E-49 288.3 6.1 126 3-132 1-129 (129)
2 PRK07034 hypothetical protein; 75.1 1.7 3.6E-05 42.4 1.7 42 177-218 61-106 (536)
3 PHA00692 hypothetical protein 52.0 5.3 0.00012 27.6 0.2 9 2-10 36-44 (74)
4 PF10873 DUF2668: Protein of u 52.0 18 0.0004 29.4 3.3 67 142-213 83-153 (155)
5 KOG4286 Dystrophin-like protei 33.6 16 0.00035 37.2 0.4 56 99-155 612-681 (966)
6 smart00265 BH4 BH4 Bcl-2 homol 32.5 35 0.00076 19.8 1.6 15 12-26 4-18 (27)
7 PF07960 CBP4: CBP4; InterPro 29.0 29 0.00064 27.6 1.1 17 10-26 30-49 (128)
8 smart00707 RPEL Repeat in Dros 28.2 40 0.00087 19.4 1.3 13 6-18 6-18 (26)
9 PF13822 ACC_epsilon: Acyl-CoA 24.6 38 0.00083 23.2 1.0 9 10-18 10-18 (62)
10 cd00952 CHBPH_aldolase Trans-o 24.4 41 0.00088 30.2 1.4 18 2-20 109-126 (309)
11 PLN02417 dihydrodipicolinate s 24.1 42 0.00091 29.6 1.4 17 3-20 103-119 (280)
12 cd00954 NAL N-Acetylneuraminic 23.8 41 0.00088 29.7 1.2 18 3-21 103-120 (288)
13 TIGR02313 HpaI-NOT-DapA 2,4-di 23.3 46 0.001 29.6 1.5 17 3-20 102-118 (294)
14 PF01473 CW_binding_1: Putativ 23.0 60 0.0013 16.6 1.3 8 58-65 7-14 (19)
15 PF08338 DUF1731: Domain of un 22.0 63 0.0014 21.0 1.6 17 5-21 31-48 (48)
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-45 Score=288.26 Aligned_cols=126 Identities=33% Similarity=0.602 Sum_probs=94.2
Q ss_pred CCCcceEcCCHHHHHHHHHHHhcC-CCCCC-CceeccccCCCCCCccccCCCCCCCCCceEEEEeccccccCCCCCcccc
Q 045278 3 NLMGYKFQPSNEQILYLLVEKRLN-PHFSH-HPIKDIVDICGLEPWDLATESTPESEDQVWYFFCEPCYKYRESHRAHRR 80 (221)
Q Consensus 3 lppGfRF~PTDeELV~~YL~~Ki~-~~~~~-~~I~~~~Dvy~~~Pw~Lp~~~~~~~~~~ewYFF~~r~~k~~~g~R~~R~ 80 (221)
|||||||+|||||||.+||++|+. .+++. .+|. ++|||++|||+|+... ..++.+||||+++++++.++.|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~-~~Diy~~~P~~L~~~~--~~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIH-DVDIYSAHPWELPAKF--KGGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSE-E--GGGS-GGGCHHHS--SS-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCccccee-ecccCccChHHhhhhc--cCCCceEEEEEecccccCCccccccc
Confidence 899999999999999999999999 44455 7899 9999999999999432 23677999999999999999999999
Q ss_pred ccceeeeecCcCeeeec-CCcceeeEEEEEeeecCCCCCCcccCeEEEEEEeC
Q 045278 81 TKAGHWKITSKDSQIKA-RNGPTGTKKFLTFYRHGLPRKEAITEWGMHEYHVK 132 (221)
Q Consensus 81 t~~G~Wk~tg~~k~I~~-~~~~iG~kktl~Fy~g~~p~g~~kT~WvMhEY~l~ 132 (221)
+++|+||++|+.+.|.+ ++.+||+|++|+||.++.+++ .+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~-~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNG-KKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS--EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCCCC-CcCCeEEEEEEeC
Confidence 99999999999999998 699999999999999888888 9999999999984
No 2
>PRK07034 hypothetical protein; Provisional
Probab=75.11 E-value=1.7 Score=42.38 Aligned_cols=42 Identities=31% Similarity=0.482 Sum_probs=29.6
Q ss_pred CCCCCCCCCCcccCCCCCCCccccccccccCCCCC----CCCCCCC
Q 045278 177 SPSDHSISNGYHSEENSPTIPQQQLQYNNSVSYPG----NPTGQNT 218 (221)
Q Consensus 177 ~~~~~s~~~~~~~~~~~~~~~~q~~~~~~~~~~~~----~~~~~~~ 218 (221)
.-.++..+..+...-+.|+..-.|.|.+++-|||+ ||+|||.
T Consensus 61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (536)
T PRK07034 61 GLADQAASGNNMARTSAPPVTLYQQQPNANDSYPNGNNNNPNGDNN 106 (536)
T ss_pred hhhhhhcccCcccccCCCCcchhhcCCCCcCCCCCCCCCCCCCCCC
Confidence 33444444555666677777788888999999876 8888863
No 3
>PHA00692 hypothetical protein
Probab=51.98 E-value=5.3 Score=27.61 Aligned_cols=9 Identities=33% Similarity=0.663 Sum_probs=7.6
Q ss_pred CCCCcceEc
Q 045278 2 ENLMGYKFQ 10 (221)
Q Consensus 2 ~lppGfRF~ 10 (221)
+.||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 579999995
No 4
>PF10873 DUF2668: Protein of unknown function (DUF2668); InterPro: IPR022640 Members in this family of proteins are annotated as cysteine and tyrosine-rich protein 1, however currently no function is known [].
Probab=51.97 E-value=18 Score=29.41 Aligned_cols=67 Identities=21% Similarity=0.294 Sum_probs=32.3
Q ss_pred EEEEEEEcCCccccCCCCCCCCCCCccccCCCCCCCCCCCCCCCC-cccCCCCCCC---ccccccccccCCCCCCC
Q 045278 142 ILCCITRKRNKKKKRGISATDEGESSQQLVSPLQQSPSDHSISNG-YHSEENSPTI---PQQQLQYNNSVSYPGNP 213 (221)
Q Consensus 142 VLCkI~~k~~~~~~~~~~~~~e~~~s~~~~s~~~~~~~~~s~~~~-~~~~~~~~~~---~~q~~~~~~~~~~~~~~ 213 (221)
-||..+++.+.++.+ ....+-.+.+++.+++|.+-+-... .+.+|.+|+- +||.+|...+-+||||+
T Consensus 83 cvCmc~kn~rgsRvg-----v~~tt~in~v~SyP~apPpysy~~e~~~~~d~PPpYsp~~~~~~~~spPppYpg~~ 153 (155)
T PF10873_consen 83 CVCMCMKNSRGSRVG-----VIRTTHINAVSSYPAAPPPYSYDHEMEYPPDLPPPYSPTPQQSAQRSPPPPYPGNS 153 (155)
T ss_pred HHhhhhhcCCCcccc-----ceeccccccccccCCCCCCccccccccccCCCCcCCCCcccccccCCCccCCCCCC
Confidence 367777777654433 1111112223345555444332211 1233433322 34455677788899975
No 5
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=33.59 E-value=16 Score=37.18 Aligned_cols=56 Identities=18% Similarity=0.191 Sum_probs=40.1
Q ss_pred CcceeeE-EEEE----------eeecCCCCCCcccCeEEEEEEeCCCCCCC-Cc--EEEEEEEEcCCcccc
Q 045278 99 NGPTGTK-KFLT----------FYRHGLPRKEAITEWGMHEYHVKDDSSYK-KE--FILCCITRKRNKKKK 155 (221)
Q Consensus 99 ~~~iG~k-ktl~----------Fy~g~~p~g~~kT~WvMhEY~l~~~~~~~-~~--~VLCkI~~k~~~~~~ 155 (221)
--|||+| |.|+ |+.|++.+| .+++.-|.||..++..+.. .+ -+||--|+.++...+
T Consensus 612 ~pIvG~RyR~l~~fn~dlCq~CF~sgraak~-hk~~~pM~Ey~~~tts~~d~rdfak~L~nkfr~~~~~a~ 681 (966)
T KOG4286|consen 612 CPIIGFRYRSLKHFNYDICQSCFFSGRAAKG-HKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRYFAK 681 (966)
T ss_pred CccceeeeeehhhcChhHHhhHhhhcccccC-CCCCCCceeeeCCCCChhhHHHHHHHHHhhhccchhhhc
Confidence 4578988 5554 677888888 9999999999998754321 23 378877776665443
No 6
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=32.45 E-value=35 Score=19.84 Aligned_cols=15 Identities=20% Similarity=0.328 Sum_probs=13.3
Q ss_pred CHHHHHHHHHHHhcC
Q 045278 12 SNEQILYLLVEKRLN 26 (221)
Q Consensus 12 TDeELV~~YL~~Ki~ 26 (221)
+-.|||.+|+.-||.
T Consensus 4 ~nRelV~~yv~yKLs 18 (27)
T smart00265 4 DNRELVVDYVTYKLS 18 (27)
T ss_pred chHHHHHHHHHHHHh
Confidence 457999999999998
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=28.99 E-value=29 Score=27.60 Aligned_cols=17 Identities=24% Similarity=0.450 Sum_probs=13.3
Q ss_pred cCCHHHHHHHH---HHHhcC
Q 045278 10 QPSNEQILYLL---VEKRLN 26 (221)
Q Consensus 10 ~PTDeELV~~Y---L~~Ki~ 26 (221)
.||||||+..| |+++..
T Consensus 30 tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 30 TPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred CCCHHHHHHhcCHHHHHHHH
Confidence 59999999987 665554
No 8
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=28.15 E-value=40 Score=19.40 Aligned_cols=13 Identities=15% Similarity=0.256 Sum_probs=11.0
Q ss_pred cceEcCCHHHHHH
Q 045278 6 GYKFQPSNEQILY 18 (221)
Q Consensus 6 GfRF~PTDeELV~ 18 (221)
...++|+-||||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
No 9
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=24.62 E-value=38 Score=23.23 Aligned_cols=9 Identities=22% Similarity=0.619 Sum_probs=7.6
Q ss_pred cCCHHHHHH
Q 045278 10 QPSNEQILY 18 (221)
Q Consensus 10 ~PTDeELV~ 18 (221)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 699999865
No 10
>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=24.42 E-value=41 Score=30.17 Aligned_cols=18 Identities=0% Similarity=-0.162 Sum_probs=14.9
Q ss_pred CCCCcceEcCCHHHHHHHH
Q 045278 2 ENLMGYKFQPSNEQILYLL 20 (221)
Q Consensus 2 ~lppGfRF~PTDeELV~~Y 20 (221)
-+|| |.|.|+++||+.||
T Consensus 109 v~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 109 LGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred ECCC-cCCCCCHHHHHHHH
Confidence 3566 56899999999988
No 11
>PLN02417 dihydrodipicolinate synthase
Probab=24.09 E-value=42 Score=29.58 Aligned_cols=17 Identities=18% Similarity=0.061 Sum_probs=14.1
Q ss_pred CCCcceEcCCHHHHHHHH
Q 045278 3 NLMGYKFQPSNEQILYLL 20 (221)
Q Consensus 3 lppGfRF~PTDeELV~~Y 20 (221)
.|| +.|.||++||+.||
T Consensus 103 ~~P-~y~~~~~~~i~~~f 119 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHF 119 (280)
T ss_pred cCC-ccCCCCHHHHHHHH
Confidence 466 55899999999988
No 12
>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=23.84 E-value=41 Score=29.67 Aligned_cols=18 Identities=17% Similarity=-0.173 Sum_probs=13.8
Q ss_pred CCCcceEcCCHHHHHHHHH
Q 045278 3 NLMGYKFQPSNEQILYLLV 21 (221)
Q Consensus 3 lppGfRF~PTDeELV~~YL 21 (221)
+||- .|.||++||+.||.
T Consensus 103 ~~P~-y~~~~~~~i~~~~~ 120 (288)
T cd00954 103 ITPF-YYKFSFEEIKDYYR 120 (288)
T ss_pred eCCC-CCCCCHHHHHHHHH
Confidence 4554 47899999999883
No 13
>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=23.27 E-value=46 Score=29.57 Aligned_cols=17 Identities=18% Similarity=0.227 Sum_probs=14.0
Q ss_pred CCCcceEcCCHHHHHHHH
Q 045278 3 NLMGYKFQPSNEQILYLL 20 (221)
Q Consensus 3 lppGfRF~PTDeELV~~Y 20 (221)
+||-| |.|+++||+.||
T Consensus 102 ~pP~y-~~~~~~~l~~~f 118 (294)
T TIGR02313 102 IVPYY-NKPNQEALYDHF 118 (294)
T ss_pred cCccC-CCCCHHHHHHHH
Confidence 45554 899999999988
No 14
>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=23.00 E-value=60 Score=16.61 Aligned_cols=8 Identities=38% Similarity=1.244 Sum_probs=6.1
Q ss_pred CceEEEEe
Q 045278 58 DQVWYFFC 65 (221)
Q Consensus 58 ~~ewYFF~ 65 (221)
+..||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 46899994
No 15
>PF08338 DUF1731: Domain of unknown function (DUF1731); InterPro: IPR013549 This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (IPR001509 from INTERPRO) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. ; PDB: 3OH8_A.
Probab=21.96 E-value=63 Score=21.00 Aligned_cols=17 Identities=35% Similarity=0.698 Sum_probs=8.9
Q ss_pred CcceEc-CCHHHHHHHHH
Q 045278 5 MGYKFQ-PSNEQILYLLV 21 (221)
Q Consensus 5 pGfRF~-PTDeELV~~YL 21 (221)
-||+|+ |+=++-+.+.|
T Consensus 31 ~GF~F~~p~l~~AL~~ll 48 (48)
T PF08338_consen 31 AGFQFRYPTLEEALRDLL 48 (48)
T ss_dssp TT---S-SSHHHHHHH--
T ss_pred CCCcccCCCHHHHHhccC
Confidence 489998 88877766543
Done!