Query 046523
Match_columns 371
No_of_seqs 154 out of 988
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 12:59:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046523.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046523hhsearch_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 7.6E-42 1.7E-46 294.4 6.4 128 10-145 1-129 (129)
2 PHA00692 hypothetical protein 22.7 35 0.00077 26.3 0.5 9 9-17 36-44 (74)
3 PF10686 DUF2493: Protein of u 21.6 59 0.0013 25.5 1.6 23 300-330 19-41 (71)
4 smart00243 GAS2 Growth-Arrest- 16.1 79 0.0017 25.4 1.2 19 295-313 49-67 (73)
5 smart00265 BH4 BH4 Bcl-2 homol 15.9 1.6E+02 0.0035 19.3 2.3 19 19-37 4-22 (27)
6 PF07960 CBP4: CBP4; InterPro 14.7 85 0.0018 27.8 1.1 14 14-27 26-40 (128)
7 PF01473 CW_binding_1: Putativ 14.3 1.1E+02 0.0025 17.5 1.3 8 66-73 7-14 (19)
8 KOG3238 Chloride ion current i 14.2 1.7E+02 0.0037 27.9 3.0 63 7-70 106-168 (216)
9 PLN02417 dihydrodipicolinate s 14.0 1.1E+02 0.0025 29.6 1.9 19 9-28 102-120 (280)
10 cd00952 CHBPH_aldolase Trans-o 13.2 1.2E+02 0.0027 29.9 2.0 18 9-27 109-126 (309)
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=7.6e-42 Score=294.40 Aligned_cols=128 Identities=53% Similarity=1.064 Sum_probs=96.2
Q ss_pred CCCCceeCCChHHHHHHHHHHhhcCCCCCc-CeeeeccCCCCCCCCcccccccCCCCCceeEEEeccCCCCCCCCccccc
Q 046523 10 VPPGFRFHPTDEELLYYYLRKKVSFEAIDL-DVIREVDLNKLEPWDLKDKCRIGSGPQNEWYFFSHKDKKYPTGTRTNRA 88 (371)
Q Consensus 10 LPpGfRF~PTDeELV~~YL~~Kv~g~pl~~-~~I~evDVy~~ePwdL~~~~~~g~g~~~eWYFFs~r~kK~~~G~R~nR~ 88 (371)
|||||||+|||+|||.+||++|+.+.+++. ++|+++|||..|||+|+... .+.+++||||+++++++.++.|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~---~~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKF---KGGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHS---SS-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhc---cCCCceEEEEEecccccCCccccccc
Confidence 899999999999999999999999999887 69999999999999999532 22457999999999999999999999
Q ss_pred ccCCeEeeccCCccEEeccccCCCCeeeEEEEEEEeecCCCCCCCCcCeEEEEEEeC
Q 046523 89 TTAGFWKATGRDKAIHITMANVNSSRRIGMRKTLVFYTGRAPHGQKTDWIMHEYRLD 145 (371)
Q Consensus 89 tggG~WK~tG~~K~I~~~~~~~~~g~~IG~KktL~Fy~gr~p~g~kT~WiMhEY~L~ 145 (371)
+++|+||.+|+.+.|... ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~-----~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDP-----GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE------TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccc-----cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999999985 5899999999999998888889999999999984
No 2
>PHA00692 hypothetical protein
Probab=22.73 E-value=35 Score=26.33 Aligned_cols=9 Identities=67% Similarity=1.412 Sum_probs=6.8
Q ss_pred CCCCCceeC
Q 046523 9 SVPPGFRFH 17 (371)
Q Consensus 9 ~LPpGfRF~ 17 (371)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 468888884
No 3
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=21.63 E-value=59 Score=25.50 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=18.4
Q ss_pred CChhHHHHHHhhcccccCCcCcccccccccC
Q 046523 300 GDWSFLDKLLTSHVHHSAQQQPDQINSHSKC 330 (371)
Q Consensus 300 ~DW~~LDkl~aS~~~~~~~~~~~~~~~~~~~ 330 (371)
.=|.+||++++.|- .+ .|+||.+
T Consensus 19 ~i~~~Ld~~~~~~~--~~------~lvhGga 41 (71)
T PF10686_consen 19 LIWAALDKVHARHP--DM------VLVHGGA 41 (71)
T ss_pred HHHHHHHHHHHhCC--CE------EEEECCC
Confidence 45899999999997 33 4999975
No 4
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=16.10 E-value=79 Score=25.39 Aligned_cols=19 Identities=37% Similarity=0.622 Sum_probs=15.9
Q ss_pred cccccCChhHHHHHHhhcc
Q 046523 295 DQRFNGDWSFLDKLLTSHV 313 (371)
Q Consensus 295 ~~~~~~DW~~LDkl~aS~~ 313 (371)
+.|+++-|-.|+.||..|-
T Consensus 49 MVRVGGGW~tL~~fL~khD 67 (73)
T smart00243 49 MVRVGGGWETLDEYLLKHD 67 (73)
T ss_pred EEEECCcHHHHHHHHHhCC
Confidence 3477899999999998874
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=15.94 E-value=1.6e+02 Score=19.28 Aligned_cols=19 Identities=26% Similarity=0.364 Sum_probs=15.3
Q ss_pred ChHHHHHHHHHHhhcCCCC
Q 046523 19 TDEELLYYYLRKKVSFEAI 37 (371)
Q Consensus 19 TDeELV~~YL~~Kv~g~pl 37 (371)
+-.|||.+|+.-|+.-...
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4689999999999886543
No 6
>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=14.74 E-value=85 Score=27.78 Aligned_cols=14 Identities=43% Similarity=0.892 Sum_probs=10.9
Q ss_pred cee-CCChHHHHHHH
Q 046523 14 FRF-HPTDEELLYYY 27 (371)
Q Consensus 14 fRF-~PTDeELV~~Y 27 (371)
|++ .||||||+..|
T Consensus 26 ~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 26 VKYTTPTEEELFKRY 40 (128)
T ss_pred heecCCCHHHHHHhc
Confidence 344 59999999875
No 7
>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=14.31 E-value=1.1e+02 Score=17.53 Aligned_cols=8 Identities=38% Similarity=1.522 Sum_probs=6.2
Q ss_pred CceeEEEe
Q 046523 66 QNEWYFFS 73 (371)
Q Consensus 66 ~~eWYFFs 73 (371)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47899994
No 8
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=14.17 E-value=1.7e+02 Score=27.92 Aligned_cols=63 Identities=21% Similarity=0.325 Sum_probs=32.7
Q ss_pred CCCCCCCceeCCChHHHHHHHHHHhhcCCCCCcCeeeeccCCCCCCCCcccccccCCCCCceeE
Q 046523 7 ELSVPPGFRFHPTDEELLYYYLRKKVSFEAIDLDVIREVDLNKLEPWDLKDKCRIGSGPQNEWY 70 (371)
Q Consensus 7 ~~~LPpGfRF~PTDeELV~~YL~~Kv~g~pl~~~~I~evDVy~~ePwdL~~~~~~g~g~~~eWY 70 (371)
.....-+|||+|+|.--+...----.....+.+....+.+-|+-+=|+.-.. ..+.|+...||
T Consensus 106 dve~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~-d~~~gDs~~~~ 168 (216)
T KOG3238|consen 106 DVEPITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAH-DAGQGDSPNSY 168 (216)
T ss_pred cccccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhh-hccCCCCcccc
Confidence 3445569999999987666432233333333333344555566665655432 23333334443
No 9
>PLN02417 dihydrodipicolinate synthase
Probab=13.96 E-value=1.1e+02 Score=29.62 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=14.9
Q ss_pred CCCCCceeCCChHHHHHHHH
Q 046523 9 SVPPGFRFHPTDEELLYYYL 28 (371)
Q Consensus 9 ~LPpGfRF~PTDeELV~~YL 28 (371)
-+|| +.|.||++||+.||-
T Consensus 102 ~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 102 HINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EcCC-ccCCCCHHHHHHHHH
Confidence 3555 668999999999873
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=13.24 E-value=1.2e+02 Score=29.90 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=14.8
Q ss_pred CCCCCceeCCChHHHHHHH
Q 046523 9 SVPPGFRFHPTDEELLYYY 27 (371)
Q Consensus 9 ~LPpGfRF~PTDeELV~~Y 27 (371)
-+|| |.|.||++||+.||
T Consensus 109 v~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 109 LGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred ECCC-cCCCCCHHHHHHHH
Confidence 4566 67999999999987
Done!