Query 026592
Match_columns 236
No_of_seqs 206 out of 876
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 10:01:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026592.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026592hhsearch_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-25 2.7E-30 180.9 7.2 84 2-85 45-129 (129)
2 PF01473 CW_binding_1: Putativ 24.0 53 0.0011 17.6 1.3 8 12-19 7-14 (19)
3 PF07491 PPI_Ypi1: Protein pho 13.3 1.6E+02 0.0034 21.3 1.9 14 104-117 37-50 (60)
4 COG3100 Uncharacterized protei 13.2 1.2E+02 0.0026 24.0 1.5 16 104-119 11-26 (103)
5 PF05865 Cypo_polyhedrin: Cypo 8.6 3.6E+02 0.0078 23.6 3.0 27 37-63 140-167 (248)
6 PF05166 YcgL: YcgL domain; I 7.9 2.5E+02 0.0054 21.0 1.5 14 106-119 1-14 (74)
7 KOG4102 Uncharacterized conser 7.0 3.6E+02 0.0077 22.1 2.1 17 104-120 63-79 (121)
8 PF08018 Antimicrobial_1: Frog 7.0 84 0.0018 18.7 -1.1 8 104-111 16-23 (24)
9 COG0616 SppA Periplasmic serin 6.4 2.5E+02 0.0054 26.0 1.0 22 34-55 139-160 (317)
10 PRK10154 hypothetical protein; 6.3 2.9E+02 0.0064 22.9 1.3 23 58-81 79-101 (134)
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=99.92 E-value=1.2e-25 Score=180.87 Aligned_cols=84 Identities=58% Similarity=1.135 Sum_probs=64.5
Q ss_pred CCCCCcCCCCCceEEEEeecCCCCCCCCCCccccCCcEEEEcccceeeec-CCeEEEEEEEEEeeeCCCCCCcccCeEEe
Q 026592 2 YENVEKAEFGEKEWYFFSPRDRKYPNGTRPNRATVSGYWKATGTDKAIYG-GSKYLGVKKALVFYKGRPPKGIKTDWIMH 80 (236)
Q Consensus 2 WdLP~~~~~ge~eWYFFspr~rk~~~G~R~nR~t~~GyWKatG~~k~I~~-~~~~VG~KktLvFy~Gr~p~g~kT~WiMh 80 (236)
|+||+....++++||||+++++++++|.|++|++++|+||++|++++|.+ ++.+||+|++|+||.++.+++.+|+|+||
T Consensus 45 ~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~ 124 (129)
T PF02365_consen 45 WELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMH 124 (129)
T ss_dssp GGCHHHSSS-SSEEEEEEE----------S-EEETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEE
T ss_pred HHhhhhccCCCceEEEEEecccccCCcccccccccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEE
Confidence 89995433467799999999999999999999999999999999999998 88999999999999998899999999999
Q ss_pred EEEeC
Q 026592 81 EYRLN 85 (236)
Q Consensus 81 EY~l~ 85 (236)
||+|.
T Consensus 125 EY~L~ 129 (129)
T PF02365_consen 125 EYSLE 129 (129)
T ss_dssp EEEE-
T ss_pred EEEeC
Confidence 99984
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=24.05 E-value=53 Score=17.65 Aligned_cols=8 Identities=38% Similarity=1.468 Sum_probs=6.3
Q ss_pred CceEEEEe
Q 026592 12 EKEWYFFS 19 (236)
Q Consensus 12 e~eWYFFs 19 (236)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 46899994
No 3
>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=13.27 E-value=1.6e+02 Score=21.31 Aligned_cols=14 Identities=29% Similarity=0.444 Sum_probs=10.8
Q ss_pred EEEEEEeeCCCCCC
Q 026592 104 VLCRIYKKRQTGSR 117 (236)
Q Consensus 104 VLCRIykK~~~~~~ 117 (236)
-+|-||.|++.-..
T Consensus 37 K~CCIyhk~~~~~e 50 (60)
T PF07491_consen 37 KCCCIYHKPRAFDE 50 (60)
T ss_pred ceeeeecCCCCCCC
Confidence 58999998876544
No 4
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=13.18 E-value=1.2e+02 Score=23.98 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=13.3
Q ss_pred EEEEEEeeCCCCCCCc
Q 026592 104 VLCRIYKKRQTGSRSV 119 (236)
Q Consensus 104 VLCRIykK~~~~~~~~ 119 (236)
-||-|||++++...++
T Consensus 11 mlCaIYkS~kk~~tYL 26 (103)
T COG3100 11 MLCAIYKSPKKDGTYL 26 (103)
T ss_pred eeeeeeecCcCCccEE
Confidence 7999999988877654
No 5
>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=8.58 E-value=3.6e+02 Score=23.56 Aligned_cols=27 Identities=26% Similarity=0.386 Sum_probs=16.9
Q ss_pred CcEEEEccc-ceeeecCCeEEEEEEEEE
Q 026592 37 SGYWKATGT-DKAIYGGSKYLGVKKALV 63 (236)
Q Consensus 37 ~GyWKatG~-~k~I~~~~~~VG~KktLv 63 (236)
+--|.+||- -+.|..+|.+||.-..|.
T Consensus 140 shpweatgikyrki~~dgeivgyshyfe 167 (248)
T PF05865_consen 140 SHPWEATGIKYRKIHRDGEIVGYSHYFE 167 (248)
T ss_dssp --S-B--GGG-EEEEETTEEEEEEEEEE
T ss_pred cCCccccCceEEEeeccceEeeeeeeee
Confidence 456999995 567888899999887664
No 6
>PF05166 YcgL: YcgL domain; InterPro: IPR007840 This family of proteins formerly called DUF709 includes the Escherichia coli gene ycgL. Homologues of YcgL are found in gammaproteobacteria. The structure of this protein shows a novel alpha/beta/alpha sandwich structure []. The proteins in this entry are functionally uncharacterised.; PDB: 2H7A_A.
Probab=7.89 E-value=2.5e+02 Score=21.01 Aligned_cols=14 Identities=29% Similarity=0.638 Sum_probs=11.1
Q ss_pred EEEEeeCCCCCCCc
Q 026592 106 CRIYKKRQTGSRSV 119 (236)
Q Consensus 106 CRIykK~~~~~~~~ 119 (236)
|-|||++++...++
T Consensus 1 C~IYkS~kK~~~YL 14 (74)
T PF05166_consen 1 CAIYKSSKKEDTYL 14 (74)
T ss_dssp EEEEEETTSSS-EE
T ss_pred CcEeecCCCCCeEE
Confidence 99999998887655
No 7
>KOG4102 consensus Uncharacterized conserved protein [Function unknown]
Probab=7.04 E-value=3.6e+02 Score=22.10 Aligned_cols=17 Identities=29% Similarity=0.348 Sum_probs=13.0
Q ss_pred EEEEEEeeCCCCCCCcc
Q 026592 104 VLCRIYKKRQTGSRSVL 120 (236)
Q Consensus 104 VLCRIykK~~~~~~~~~ 120 (236)
-.|-||+|++.-..+..
T Consensus 63 KcCCIy~kpr~~~esSs 79 (121)
T KOG4102|consen 63 KCCCIYHKPRAFDESSS 79 (121)
T ss_pred ceeEEEeCccccCcccc
Confidence 68999999988765433
No 8
>PF08018 Antimicrobial_1: Frog antimicrobial peptide ; InterPro: IPR012520 This family includes antimicrobial peptides secreted from skins of frogs. The secretion of antimicrobial peptides from the skins of frogs plays an important role in the self defence of these frogs. Structural characterisation of these peptides showed that they belonged to four known families: the brevinin-1 family, the esculentin-2 family, the ranatuerin-2 family and the temporin family [].; GO: 0005576 extracellular region
Probab=6.98 E-value=84 Score=18.67 Aligned_cols=8 Identities=50% Similarity=1.020 Sum_probs=6.6
Q ss_pred EEEEEEee
Q 026592 104 VLCRIYKK 111 (236)
Q Consensus 104 VLCRIykK 111 (236)
++|.|.||
T Consensus 16 i~C~ItKK 23 (24)
T PF08018_consen 16 IFCAITKK 23 (24)
T ss_pred hHhhhccc
Confidence 78998876
No 9
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=6.39 E-value=2.5e+02 Score=26.04 Aligned_cols=22 Identities=32% Similarity=0.442 Sum_probs=17.4
Q ss_pred ccCCcEEEEcccceeeecCCeE
Q 026592 34 ATVSGYWKATGTDKAIYGGSKY 55 (236)
Q Consensus 34 ~t~~GyWKatG~~k~I~~~~~~ 55 (236)
++.+|||-+...++.|.+...+
T Consensus 139 AASGGY~IA~aAd~I~a~p~si 160 (317)
T COG0616 139 AASGGYYIALAADKIVADPSSI 160 (317)
T ss_pred ecchhhhhhccCCEEEecCCce
Confidence 4569999999999998775443
No 10
>PRK10154 hypothetical protein; Provisional
Probab=6.28 E-value=2.9e+02 Score=22.88 Aligned_cols=23 Identities=26% Similarity=0.385 Sum_probs=15.3
Q ss_pred EEEEEEeeeCCCCCCcccCeEEeE
Q 026592 58 VKKALVFYKGRPPKGIKTDWIMHE 81 (236)
Q Consensus 58 ~KktLvFy~Gr~p~g~kT~WiMhE 81 (236)
-.++|.||+. -.++..|+|+---
T Consensus 79 ~s~tl~f~~~-lk~~q~T~W~~~~ 101 (134)
T PRK10154 79 ASQSLNIPSE-IKEGQTTDWININ 101 (134)
T ss_pred CceEEecchh-hccCCccccEEcc
Confidence 3477777753 2457899998543
Done!