Query 030168
Match_columns 182
No_of_seqs 166 out of 801
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 09:35:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030168.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030168hhsearch_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 2.7E-24 5.8E-29 165.0 8.2 76 2-80 54-129 (129)
2 PF01473 CW_binding_1: Putativ 33.5 29 0.00064 17.5 1.3 9 3-11 7-15 (19)
3 PF15536 Toxin_58: Putative to 20.0 1.1E+02 0.0023 23.6 2.7 13 98-110 98-110 (131)
4 KOG4095 Uncharacterized conser 14.0 5.7E+02 0.012 20.6 5.5 13 133-145 82-94 (165)
5 COG5628 Predicted acetyltransf 12.8 2E+02 0.0044 22.5 2.6 49 31-84 30-78 (143)
6 COG3100 Uncharacterized protei 12.3 1.4E+02 0.003 22.3 1.5 16 100-115 9-24 (103)
7 PF07491 PPI_Ypi1: Protein pho 12.3 1.3E+02 0.0028 20.4 1.3 11 102-112 37-47 (60)
8 KOG3761 Choline transporter [L 12.0 1.1E+02 0.0024 28.2 1.0 37 67-108 299-335 (591)
9 PF02402 Lysis_col: Lysis prot 11.8 1E+02 0.0022 19.8 0.6 12 158-169 33-44 (46)
10 PF05865 Cypo_polyhedrin: Cypo 11.1 2.7E+02 0.0059 23.0 3.0 28 30-59 140-168 (248)
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=99.91 E-value=2.7e-24 Score=165.03 Aligned_cols=76 Identities=39% Similarity=0.776 Sum_probs=58.2
Q ss_pred CCceEEEeecCCCCccccCCCccccccCCeeeeecCCceeEEeCCCceEEEEEEEEEeeeccCCCCcccCeEEEEEEeC
Q 030168 2 KEKKRYFFSNIRNESAIDNDGKCKIAAGSGYWKPVGKNRQILASGTKQVVGIRKTLIFCEGKRGHETKTQWVMHQYHLV 80 (182)
Q Consensus 2 ~e~ewYFFs~~rr~~k~~~g~R~~R~t~~GyWK~tG~~k~I~~~~~g~~VG~KktLvFy~gk~~~g~rT~WvMhEY~L~ 80 (182)
++.+||||++ ++.++.+|.|.+|++++|+||++|++++|... ++.+||+|++|+||.++.+++.+|+|+||||+|.
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 GDEEWYFFSP--RKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp -SSEEEEEEE------------S-EEETTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred CCceEEEEEe--cccccCCcccccccccceEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 3679999999 77888899999999999999999999999954 8999999999999999888899999999999983
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=33.52 E-value=29 Score=17.53 Aligned_cols=9 Identities=22% Similarity=0.752 Sum_probs=6.7
Q ss_pred CceEEEeec
Q 030168 3 EKKRYFFSN 11 (182)
Q Consensus 3 e~ewYFFs~ 11 (182)
++.||||..
T Consensus 7 ~~~wYy~~~ 15 (19)
T PF01473_consen 7 NGNWYYFDS 15 (19)
T ss_dssp TTEEEEETT
T ss_pred CCEEEEeCC
Confidence 468999954
No 3
>PF15536 Toxin_58: Putative toxin 58
Probab=20.04 E-value=1.1e+02 Score=23.56 Aligned_cols=13 Identities=8% Similarity=0.161 Sum_probs=9.2
Q ss_pred eCcEEEEEEEEcC
Q 030168 98 IGDWVVYRIFQRK 110 (182)
Q Consensus 98 ~~~~VLCRIf~K~ 110 (182)
-+.-|||||+..-
T Consensus 98 GnHkiiCkv~~~a 110 (131)
T PF15536_consen 98 GNHKIICKVTPRA 110 (131)
T ss_pred CCceEEEEeccCC
Confidence 3456999988653
No 4
>KOG4095 consensus Uncharacterized conserved protein (tumor-specific protein BCL7 in humans) [General function prediction only]
Probab=14.00 E-value=5.7e+02 Score=20.62 Aligned_cols=13 Identities=23% Similarity=0.340 Sum_probs=8.5
Q ss_pred CcceEEecccccc
Q 030168 133 NQLQVIDFSVIEA 145 (182)
Q Consensus 133 ~~~~~~df~~~~~ 145 (182)
+.+.++||--++.
T Consensus 82 ~s~~lld~~denS 94 (165)
T KOG4095|consen 82 NSSLLLDFQDENS 94 (165)
T ss_pred Ccccccccccccc
Confidence 4666778776654
No 5
>COG5628 Predicted acetyltransferase [General function prediction only]
Probab=12.80 E-value=2e+02 Score=22.52 Aligned_cols=49 Identities=14% Similarity=0.212 Sum_probs=34.0
Q ss_pred eeeeecCCceeEEeCCCceEEEEEEEEEeeeccCCCCcccCeEEEEEEeCCccc
Q 030168 31 GYWKPVGKNRQILASGTKQVVGIRKTLIFCEGKRGHETKTQWVMHQYHLVAIAT 84 (182)
Q Consensus 31 GyWK~tG~~k~I~~~~~g~~VG~KktLvFy~gk~~~g~rT~WvMhEY~L~~~~~ 84 (182)
-||...|..--.+ .-++.+||+--.| .++-...+.+|-|-||-+.....
T Consensus 30 ~~w~~~~~~~~~~-~~~~~~igf~l~L----~~~~~~~~iD~~~~efFIi~k~~ 78 (143)
T COG5628 30 TYWRDPVREAWLF-RIGGLPVGFALVL----DLAHSPTPIDRAVAEFFIVRKHR 78 (143)
T ss_pred hhhcCcccceeEE-EECCceeeeeeee----cccCCCCcccccchheEeeehhh
Confidence 4788887655433 2577899965444 34444578999999999987643
No 6
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=12.33 E-value=1.4e+02 Score=22.28 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=12.0
Q ss_pred cEEEEEEEEcCCCCCC
Q 030168 100 DWVVYRIFQRKKKPKK 115 (182)
Q Consensus 100 ~~VLCRIf~K~~~~~~ 115 (182)
--.||-||+.+++...
T Consensus 9 ~~mlCaIYkS~kk~~t 24 (103)
T COG3100 9 KSMLCAIYKSPKKDGT 24 (103)
T ss_pred eeeeeeeeecCcCCcc
Confidence 4479999998776554
No 7
>PF07491 PPI_Ypi1: Protein phosphatase inhibitor ; InterPro: IPR011107 These proteins include Ypi1, a novel Saccharomyces cerevisiae type 1 protein phosphatase inhibitor [] and ppp1r11/hcgv (O60927 from SWISSPROT), annotated as having protein phosphatase inhibitor activity [].
Probab=12.30 E-value=1.3e+02 Score=20.41 Aligned_cols=11 Identities=9% Similarity=0.313 Sum_probs=8.5
Q ss_pred EEEEEEEcCCC
Q 030168 102 VVYRIFQRKKK 112 (182)
Q Consensus 102 VLCRIf~K~~~ 112 (182)
=+|.||.|++.
T Consensus 37 K~CCIyhk~~~ 47 (60)
T PF07491_consen 37 KCCCIYHKPRA 47 (60)
T ss_pred ceeeeecCCCC
Confidence 48999998743
No 8
>KOG3761 consensus Choline transporter [Lipid transport and metabolism]
Probab=11.98 E-value=1.1e+02 Score=28.23 Aligned_cols=37 Identities=24% Similarity=0.326 Sum_probs=24.4
Q ss_pred CcccCeEEEEEEeCCcccCCCCCccccceeeeCcEEEEEEEE
Q 030168 67 ETKTQWVMHQYHLVAIATNTNLTQPVFKMVIIGDWVVYRIFQ 108 (182)
Q Consensus 67 g~rT~WvMhEY~L~~~~~~~~~~~~~~~~~~~~~~VLCRIf~ 108 (182)
+..|+|-|..|.+.++.....+-+ ++..+.+|--||+
T Consensus 299 ~~ntdw~~t~y~~~d~~tkvesip-----~d~~dmilpiv~q 335 (591)
T KOG3761|consen 299 AANTDWNMTAYGLPDNGTKVESIP-----PDEADMILPIVFQ 335 (591)
T ss_pred hccCcccccccCCCCCCcccccCC-----ccccceehhHHHH
Confidence 567999999999999876543322 2445555554443
No 9
>PF02402 Lysis_col: Lysis protein; InterPro: IPR003059 The DNA sequence of the entire colicin E2 operon has been determined []. The operon comprises the colicin activity gene (ceaB), the colicin immunity gene (ceiB) and the lysis gene (celB), which is essential for colicin release from producing cells []. A putative LexA binding site is located upstream from ceaB, and a rho-independent terminator structure is located downstream from celB []. Comparison of the amino acid sequences of colicin E2 and cloacin DF13 reveal extensive similarity. These colicins have different modes of action and recognise different cell surface receptors; the two major regions of heterology at the C terminus, and in the C-terminal end of the central region are thought to correspond to the catalytic and receptor-recognition domains, respectively []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. By contrast, the lysis proteins of the ColE2, ColE1 and CloDF13 plasmids are almost identical except in the N-terminal regions, which themselves are similar to lipoprotein signal peptides []. Processing of the ColE2 prolysis protein to the mature form is prevented by globomycin, a specific inhibitor of the lipoprotein signal peptidase []. The mature ColE2 lysis protein is located in the cell envelope [].; GO: 0009405 pathogenesis, 0019835 cytolysis, 0019867 outer membrane
Probab=11.83 E-value=1e+02 Score=19.81 Aligned_cols=12 Identities=42% Similarity=0.382 Sum_probs=7.9
Q ss_pred CCCCCCcccccc
Q 030168 158 VSSCSSEITADE 169 (182)
Q Consensus 158 ~ss~ss~it~~~ 169 (182)
+||+||.+|.++
T Consensus 33 aPSSss~lTGv~ 44 (46)
T PF02402_consen 33 APSSSSELTGVA 44 (46)
T ss_pred CCCccceeeeee
Confidence 445577788765
No 10
>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=11.08 E-value=2.7e+02 Score=22.97 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=16.5
Q ss_pred CeeeeecCC-ceeEEeCCCceEEEEEEEEEe
Q 030168 30 SGYWKPVGK-NRQILASGTKQVVGIRKTLIF 59 (182)
Q Consensus 30 ~GyWK~tG~-~k~I~~~~~g~~VG~KktLvF 59 (182)
+--|.+||. -+.|. .+|++||.-..|..
T Consensus 140 shpweatgikyrki~--~dgeivgyshyfel 168 (248)
T PF05865_consen 140 SHPWEATGIKYRKIH--RDGEIVGYSHYFEL 168 (248)
T ss_dssp --S-B--GGG-EEEE--ETTEEEEEEEEEE-
T ss_pred cCCccccCceEEEee--ccceEeeeeeeeec
Confidence 567999995 56676 78999998776643
Done!