Query 035726
Match_columns 101
No_of_seqs 107 out of 710
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 05:51:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035726.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035726hhsearch_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 9.6E-27 2.1E-31 155.4 9.0 78 4-82 52-129 (129)
2 PF01473 CW_binding_1: Putativ 58.6 8.2 0.00018 16.9 1.4 8 7-14 7-14 (19)
3 cd01785 PDZ_GEF_RA Ubiquitin-l 39.2 12 0.00026 23.4 0.4 24 72-99 29-52 (85)
4 KOG3761 Choline transporter [L 29.3 26 0.00056 28.0 0.8 27 68-94 298-330 (591)
5 PF09866 DUF2093: Uncharacteri 27.1 57 0.0012 17.8 1.7 10 89-98 4-13 (42)
6 COG3908 Uncharacterized protei 21.0 1.1E+02 0.0024 18.5 2.3 10 88-97 26-35 (77)
7 PF14709 DND1_DSRM: double str 16.0 1.3E+02 0.0028 18.1 1.9 29 71-99 13-41 (80)
8 PF05865 Cypo_polyhedrin: Cypo 15.6 2.2E+02 0.0047 20.4 3.2 28 32-61 140-168 (248)
9 COG5127 Vacuolar H+-ATPase V1 12.5 2E+02 0.0044 22.6 2.5 14 87-100 216-229 (383)
10 KOG2909 Vacuolar H+-ATPase V1 12.0 2E+02 0.0044 22.8 2.4 14 87-100 218-231 (381)
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=99.94 E-value=9.6e-27 Score=155.42 Aligned_cols=78 Identities=51% Similarity=0.883 Sum_probs=59.4
Q ss_pred CCCCCeEEEEEeccccccCCCcceeeccccEEEEcCcceeEEcCCCCeEEEEEEEeEeeeCCCCCCCccCeEEEEEEeC
Q 035726 4 TPDDEEWYFFSELQKKYANSDRVDRTTKVGSWKVTGGDRQIWDNCGKEVIGVKKNLVFHKGHGSKAKKTSWVIHEYHSS 82 (101)
Q Consensus 4 ~~~~~~wYFFs~~~~k~~~g~r~~R~~~~G~Wk~~g~~~~I~~~~~g~~vG~kk~l~f~~g~~~~~~kT~W~M~EY~l~ 82 (101)
..++++||||++++.++.++.|.+|++++|+||.+|+.++|.+. ++.+||.|++|+||.++.+++.+|+|+||||+|.
T Consensus 52 ~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 52 KGGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp SS-SSEEEEEEE----------S-EEETTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cCCCceEEEEEecccccCCcccccccccceEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 35678999999999999999999999999999999999999985 8889999999999999889999999999999984
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=58.56 E-value=8.2 Score=16.95 Aligned_cols=8 Identities=38% Similarity=1.535 Sum_probs=6.5
Q ss_pred CCeEEEEE
Q 035726 7 DEEWYFFS 14 (101)
Q Consensus 7 ~~~wYFFs 14 (101)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 58899994
No 3
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=39.17 E-value=12 Score=23.38 Aligned_cols=24 Identities=8% Similarity=0.124 Sum_probs=16.3
Q ss_pred cCeEEEEEEeCCCCCCCCCCeEEEEEEE
Q 035726 72 TSWVIHEYHSSKASIHQAISSVLYNLFF 99 (101)
Q Consensus 72 T~W~M~EY~l~~~~~~~~~~~VlCki~~ 99 (101)
+.-.|+||.+..+ ..+|.||.|-+
T Consensus 29 v~lal~eFgi~~~----s~~~sLceVtV 52 (85)
T cd01785 29 VMLALQEFGITAP----SSNFSLCEVSV 52 (85)
T ss_pred HHHHHHHhCCCCC----ccceEEEEEEe
Confidence 3455777877654 57888888754
No 4
>KOG3761 consensus Choline transporter [Lipid transport and metabolism]
Probab=29.30 E-value=26 Score=28.02 Aligned_cols=27 Identities=19% Similarity=0.345 Sum_probs=19.8
Q ss_pred CCCccCeEEEEEEeCCCCC------CCCCCeEE
Q 035726 68 KAKKTSWVIHEYHSSKASI------HQAISSVL 94 (101)
Q Consensus 68 ~~~kT~W~M~EY~l~~~~~------~~~~~~Vl 94 (101)
-+..|+|-|..|.+.++.. |++.+.+|
T Consensus 298 i~~ntdw~~t~y~~~d~~tkvesip~d~~dmil 330 (591)
T KOG3761|consen 298 IAANTDWNMTAYGLPDNGTKVESIPPDEADMIL 330 (591)
T ss_pred hhccCcccccccCCCCCCcccccCCccccceeh
Confidence 3568999999999988653 34556554
No 5
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=27.07 E-value=57 Score=17.80 Aligned_cols=10 Identities=20% Similarity=-0.157 Sum_probs=8.1
Q ss_pred CCCeEEEEEE
Q 035726 89 AISSVLYNLF 98 (101)
Q Consensus 89 ~~~~VlCki~ 98 (101)
.++||+|-|-
T Consensus 4 pG~~V~CAVT 13 (42)
T PF09866_consen 4 PGSFVRCAVT 13 (42)
T ss_pred CCCEEEEEee
Confidence 5899999873
No 6
>COG3908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.98 E-value=1.1e+02 Score=18.55 Aligned_cols=10 Identities=30% Similarity=0.129 Sum_probs=7.6
Q ss_pred CCCCeEEEEE
Q 035726 88 QAISSVLYNL 97 (101)
Q Consensus 88 ~~~~~VlCki 97 (101)
..+.+|||-|
T Consensus 26 ~~GsfV~CAV 35 (77)
T COG3908 26 SPGSFVLCAV 35 (77)
T ss_pred cCCcEEEEEe
Confidence 3578899976
No 7
>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1
Probab=15.95 E-value=1.3e+02 Score=18.14 Aligned_cols=29 Identities=21% Similarity=0.257 Sum_probs=20.8
Q ss_pred ccCeEEEEEEeCCCCCCCCCCeEEEEEEE
Q 035726 71 KTSWVIHEYHSSKASIHQAISSVLYNLFF 99 (101)
Q Consensus 71 kT~W~M~EY~l~~~~~~~~~~~VlCki~~ 99 (101)
+-.|-+-+|.+....-|+....-+|||..
T Consensus 13 k~~W~~P~y~l~~~~Gp~~~~~F~ykV~i 41 (80)
T PF14709_consen 13 KNKWGPPVYELVSESGPDHRKLFLYKVVI 41 (80)
T ss_pred hcCCCCCeEEEEeccCCCccEEEEEEEEE
Confidence 56788888988755445556678888864
No 8
>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=15.57 E-value=2.2e+02 Score=20.38 Aligned_cols=28 Identities=25% Similarity=0.518 Sum_probs=17.4
Q ss_pred ccEEEEcCcc-eeEEcCCCCeEEEEEEEeEe
Q 035726 32 VGSWKVTGGD-RQIWDNCGKEVIGVKKNLVF 61 (101)
Q Consensus 32 ~G~Wk~~g~~-~~I~~~~~g~~vG~kk~l~f 61 (101)
+--|.++|-. +.|.. +|++||.-..|..
T Consensus 140 shpweatgikyrki~~--dgeivgyshyfel 168 (248)
T PF05865_consen 140 SHPWEATGIKYRKIHR--DGEIVGYSHYFEL 168 (248)
T ss_dssp --S-B--GGG-EEEEE--TTEEEEEEEEEE-
T ss_pred cCCccccCceEEEeec--cceEeeeeeeeec
Confidence 3459999975 56765 8999999887765
No 9
>COG5127 Vacuolar H+-ATPase V1 sector, subunit C [Energy production and conversion]
Probab=12.55 E-value=2e+02 Score=22.56 Aligned_cols=14 Identities=21% Similarity=0.572 Sum_probs=12.1
Q ss_pred CCCCCeEEEEEEEE
Q 035726 87 HQAISSVLYNLFFF 100 (101)
Q Consensus 87 ~~~~~~VlCki~~~ 100 (101)
.++.+|||.+|++|
T Consensus 216 ~~D~EyvLf~V~vf 229 (383)
T COG5127 216 NSDEEYVLFKVYVF 229 (383)
T ss_pred cCccceEEEEEEEE
Confidence 36789999999987
No 10
>KOG2909 consensus Vacuolar H+-ATPase V1 sector, subunit C [Energy production and conversion]
Probab=12.03 E-value=2e+02 Score=22.77 Aligned_cols=14 Identities=21% Similarity=0.517 Sum_probs=12.1
Q ss_pred CCCCCeEEEEEEEE
Q 035726 87 HQAISSVLYNLFFF 100 (101)
Q Consensus 87 ~~~~~~VlCki~~~ 100 (101)
..+.+|+||+|++|
T Consensus 218 ~eD~Ey~Lf~V~lF 231 (381)
T KOG2909|consen 218 NEDAEYVLFTVTLF 231 (381)
T ss_pred ccccceEEEEEEEe
Confidence 35789999999987
Done!