Query 036376
Match_columns 275
No_of_seqs 211 out of 820
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 12:05:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036376hhsearch_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 99.9 1.2E-23 2.6E-28 171.9 7.7 75 5-79 54-129 (129)
2 PF01473 CW_binding_1: Putativ 16.8 92 0.002 17.6 1.3 8 6-13 7-14 (19)
3 PF14799 FAM195: FAM195 family 13.4 36 0.00077 27.8 -1.5 10 266-275 80-89 (99)
4 PF05865 Cypo_polyhedrin: Cypo 11.9 2.7E+02 0.0059 25.5 3.5 27 32-58 141-168 (248)
5 PRK10154 hypothetical protein; 10.4 2.8E+02 0.0061 24.1 3.0 21 53-74 80-100 (134)
6 PF10807 DUF2541: Protein of u 8.6 4E+02 0.0087 23.2 3.2 22 52-74 79-100 (134)
7 PF10287 DUF2401: Putative TOS 7.5 2.8E+02 0.006 26.3 1.9 44 212-256 8-60 (235)
8 cd01826 acyloxyacyl_hydrolase_ 5.4 4E+02 0.0087 26.0 1.8 25 185-209 56-85 (305)
9 COG0616 SppA Periplasmic serin 5.0 3.5E+02 0.0076 25.9 1.2 22 28-49 139-160 (317)
10 cd08543 SAM_PNT-ETS-2 Sterile 4.8 58 0.0012 26.3 -3.6 28 69-96 31-58 (89)
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=99.89 E-value=1.2e-23 Score=171.93 Aligned_cols=75 Identities=60% Similarity=1.212 Sum_probs=58.9
Q ss_pred CCceEEEeeecCCCCCCCCCccccCCCCeeEeecCceeEee-CCEEEEEEEEEEeeeccCCCCCccceEEEEEEeC
Q 036376 5 GEKEWYFFNLRDRKYPTGLRTNRATEAGYWKTTGKDKEIFR-AGVLVGMKKTLVFYKGRAPKGEKSNWVMHEYRLE 79 (275)
Q Consensus 5 gekEWYFFSpR~rKy~~G~R~nRaTg~GyWKatGkdK~I~~-~g~lVG~KKTLvFY~GraP~G~KT~WVMHEYrL~ 79 (275)
++++|||||++++++.+|.|.+|++++|+||++|++++|.. ++.+||+||+|+||.++.+++.+|+|+||||+|.
T Consensus 54 ~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 54 GDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp -SSEEEEEEE----------S-EEETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred CCceEEEEEecccccCCcccccccccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 57799999999999999999999999999999999999998 8999999999999999889999999999999984
No 2
>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=16.76 E-value=92 Score=17.64 Aligned_cols=8 Identities=38% Similarity=1.539 Sum_probs=6.5
Q ss_pred CceEEEee
Q 036376 6 EKEWYFFN 13 (275)
Q Consensus 6 ekEWYFFS 13 (275)
+..||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899994
No 3
>PF14799 FAM195: FAM195 family
Probab=13.42 E-value=36 Score=27.77 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=9.0
Q ss_pred cCCCCCCCCC
Q 036376 266 EQPFNLDSIW 275 (275)
Q Consensus 266 ~~~~~~~~~~ 275 (275)
=.|||||+.|
T Consensus 80 FkPfDLE~wW 89 (99)
T PF14799_consen 80 FKPFDLEEWW 89 (99)
T ss_pred CcccCHHHHH
Confidence 7899999988
No 4
>PF05865 Cypo_polyhedrin: Cypovirus polyhedrin protein; InterPro: IPR008464 This family consists of several Cypovirus polyhedrin proteins. Polyhedrin is known to form a crystalline matrix (polyhedra) in infected insect cells [].; PDB: 2OH7_A 2OH5_A 2OH6_A.
Probab=11.87 E-value=2.7e+02 Score=25.55 Aligned_cols=27 Identities=33% Similarity=0.635 Sum_probs=17.4
Q ss_pred CeeEeec-CceeEeeCCEEEEEEEEEEe
Q 036376 32 GYWKTTG-KDKEIFRAGVLVGMKKTLVF 58 (275)
Q Consensus 32 GyWKatG-kdK~I~~~g~lVG~KKTLvF 58 (275)
--|.+|| +-+.|..+|.+||.--.|..
T Consensus 141 hpweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 141 HPWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp -S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred CCccccCceEEEeeccceEeeeeeeeec
Confidence 4699999 46778889999998877654
No 5
>PRK10154 hypothetical protein; Provisional
Probab=10.42 E-value=2.8e+02 Score=24.14 Aligned_cols=21 Identities=14% Similarity=0.428 Sum_probs=15.2
Q ss_pred EEEEEeeeccCCCCCccceEEE
Q 036376 53 KKTLVFYKGRAPKGEKSNWVMH 74 (275)
Q Consensus 53 KKTLvFY~GraP~G~KT~WVMH 74 (275)
.++|.||+. -.+++.|+|+--
T Consensus 80 s~tl~f~~~-lk~~q~T~W~~~ 100 (134)
T PRK10154 80 SQSLNIPSE-IKEGQTTDWINI 100 (134)
T ss_pred ceEEecchh-hccCCccccEEc
Confidence 378888763 356889999853
No 6
>PF10807 DUF2541: Protein of unknown function (DUF2541); InterPro: IPR020240 This entry represents proteins found in the Gammaproteobacteria that have no known function.
Probab=8.59 E-value=4e+02 Score=23.23 Aligned_cols=22 Identities=23% Similarity=0.542 Sum_probs=15.3
Q ss_pred EEEEEEeeeccCCCCCccceEEE
Q 036376 52 MKKTLVFYKGRAPKGEKSNWVMH 74 (275)
Q Consensus 52 ~KKTLvFY~GraP~G~KT~WVMH 74 (275)
--++|.||.. -..|..|+|+--
T Consensus 79 ~s~~l~~~~~-ikeg~tT~Wi~i 100 (134)
T PF10807_consen 79 ESQTLNFPRS-IKEGQTTDWINI 100 (134)
T ss_pred cceEEccccc-ccCCCccCcEEe
Confidence 3478888763 356889999843
No 7
>PF10287 DUF2401: Putative TOS1-like glycosyl hydrolase (DUF2401); InterPro: IPR018805 This entry represents a family of proteins conserved primarily in fungi. One member is annotated putatively as OPEL, a house-keeping protein, but this could not be confirmed. It contains 5 highly conserved cysteines two of which form a characteristic CGC sequence motif.
Probab=7.46 E-value=2.8e+02 Score=26.27 Aligned_cols=44 Identities=30% Similarity=0.440 Sum_probs=29.8
Q ss_pred chhhhhhhccccCccccccCC-----ccccccCCC---Cc-cccccccceeecc
Q 036376 212 NYQAREATSNEHNSFLQQQGG-----INSRFESDL---SS-NFQASSSSKVILD 256 (275)
Q Consensus 212 ~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~---~~-~~~~~~~~~~~~~ 256 (275)
.|+.....+.+...||-..|| .++-||.-| ++ ....++|+.+ |+
T Consensus 8 ayY~a~~g~a~n~tFLnn~Gg~gSGv~s~~~Gnslsya~sdG~~~assp~~-l~ 60 (235)
T PF10287_consen 8 AYYNASSGTADNLTFLNNYGGDGSGVWSSCFGNSLSYANSDGTGGASSPTV-LK 60 (235)
T ss_pred EEEECCCCcccCeEEeCCCCCCCccccccccCccceeeccCCCcccCCCcc-cC
Confidence 455445556777899998888 677799888 33 4445556666 66
No 8
>cd01826 acyloxyacyl_hydrolase_like Acyloxyacyl-hydrolase like subfamily of the SGNH-hydrolase family. Acyloxyacyl-hydrolase is a leukocyte-secreted enzyme that deacetylates bacterial lipopolysaccharides.
Probab=5.43 E-value=4e+02 Score=26.02 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCCC-----CchhHHHHHHhh
Q 036376 185 PSLTWPSSLLSPN-----LSMNSLLLKALQ 209 (275)
Q Consensus 185 ~~~~~~~~~~~~~-----~~~~~~~~~~~~ 209 (275)
|++.|..|.+++. ..++|+-++.+.
T Consensus 56 p~~s~~TG~~~~~~~~~~~~~~S~y~rl~~ 85 (305)
T cd01826 56 PMLSGATGFANSTRYIIGGFTDSLYLRLRE 85 (305)
T ss_pred ccccccccCCcccccccCCccccHHHHHhh
Confidence 8899999998765 589999888776
No 9
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=5.05 E-value=3.5e+02 Score=25.86 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=17.6
Q ss_pred cCCCCeeEeecCceeEeeCCEE
Q 036376 28 ATEAGYWKTTGKDKEIFRAGVL 49 (275)
Q Consensus 28 aTg~GyWKatGkdK~I~~~g~l 49 (275)
++.+|||-+...++-|.+...+
T Consensus 139 AASGGY~IA~aAd~I~a~p~si 160 (317)
T COG0616 139 AASGGYYIALAADKIVADPSSI 160 (317)
T ss_pred ecchhhhhhccCCEEEecCCce
Confidence 4689999999999998865433
No 10
>cd08543 SAM_PNT-ETS-2 Sterile alpha motif (SAM)/Pointed domain of ETS-2. SAM Pointed domain of ETS-2 subfamily of ETS transcriptional regulators is a protein-protein interaction domain. It contains a docking site for Cdk10 (cyclin-dependent kinase 10), a member of the Cdc2 kinase family. The interaction between ETS-2 and Cdk10 kinase inhibits ETS-2 transactivation activity in mammals. ETS-2 is also regulated by ERK2 MAP kinase. ETS-2, which is phosphorylated by ERK2, can interact with coactivators and enhance transactivation. ETS-2 transcriptional activators are involved in embryonic development and cell cycle control. The Ets-2 gene is a proto-oncogene. It is overexpressed in breast and prostate cancer cells and its overexpression is necessary for transformation of such cells. Members of ETS-2 subfamily are potential molecular targets for selective cancer therapy.
Probab=4.79 E-value=58 Score=26.35 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=17.7
Q ss_pred cceEEEEEEeCCCCCCCCCCCCeEEEEE
Q 036376 69 SNWVMHEYRLENKHPFRSSKEEWVVCRV 96 (275)
Q Consensus 69 T~WVMHEYrL~~~~~~~~~~~ewVLCRV 96 (275)
-.|.|+||.|..-....-..+.-.||++
T Consensus 31 L~Wa~~ef~L~~i~~~~F~m~Gk~LC~L 58 (89)
T cd08543 31 LLWATNEFSLVNVNFQQFGMNGQELCNL 58 (89)
T ss_pred HHHHHHHcCCCCCCcccCCCChHHHHcC
Confidence 3599999999875432223344456665
Done!