Query 032247
Match_columns 144
No_of_seqs 115 out of 833
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 11:33:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032247.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032247hhsearch_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 3.4E-47 7.5E-52 270.3 7.3 126 5-135 1-129 (129)
2 PHA00692 hypothetical protein 60.2 3.4 7.3E-05 25.4 0.3 9 4-12 36-44 (74)
3 KOG3238 Chloride ion current i 39.9 32 0.00068 26.4 2.8 61 5-66 109-170 (216)
4 PF01473 CW_binding_1: Putativ 31.7 37 0.0008 15.4 1.3 8 60-67 7-14 (19)
5 PF05865 Cypo_polyhedrin: Cypo 27.6 79 0.0017 23.6 3.1 27 86-112 141-168 (248)
6 smart00265 BH4 BH4 Bcl-2 homol 26.0 94 0.002 15.9 2.3 19 14-32 4-23 (27)
7 COG3908 Uncharacterized protei 23.5 46 0.001 21.1 1.1 20 125-144 15-34 (77)
8 PF10107 Endonuc_Holl: Endonuc 19.7 40 0.00087 24.7 0.3 13 4-16 84-96 (156)
9 PRK14390 hypothetical protein; 18.8 53 0.0011 20.4 0.6 12 5-16 13-24 (63)
10 COG4741 Predicted secreted end 18.3 46 0.001 24.5 0.3 15 4-18 97-112 (175)
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=3.4e-47 Score=270.29 Aligned_cols=126 Identities=35% Similarity=0.617 Sum_probs=95.1
Q ss_pred CCCCceEcCCHH-HHHHHHhhhhCCCCCCC-CCeeccCCCCCCCCCCccccccCCCCCCeEEEEecccccccCCCccccc
Q 032247 5 MGQGYKFQPSDE-LIVSLLKEKRLDPHFLY-GPIKDIGHICNLEPGDLATESETDSEDRACYFFYEPRYKYRNSNRVHRR 82 (144)
Q Consensus 5 lp~G~rF~Ptde-Li~~YL~~k~~g~~l~~-~~I~~~~Dvy~~~P~~L~~~~~~~~~~~~~yFF~~~~~~~~~g~r~~r~ 82 (144)
|||||||+|||+ ||.+||.+|+.|.+++. ++|+++ |||++|||+|+... .+++.+||||+++++++.+++|.+|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~-Diy~~~P~~L~~~~--~~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDV-DIYSAHPWELPAKF--KGGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE---GGGS-GGGCHHHS--SS-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeec-ccCccChHHhhhhc--cCCCceEEEEEecccccCCccccccc
Confidence 899999999999 99999999999999887 799999 99999999999422 23667999999999999999999999
Q ss_pred ccCceeEeecCCceEee-CCcEEEEEEEEEEEecCCCCCCCcCCCeEEEEEEeC
Q 032247 83 AEAGHWKITSEDSQIEA-SNGLIGTKKFLTFYRRSPGSKVPVKTDWVMHEYHVK 135 (144)
Q Consensus 83 ~~~G~W~~~g~~~~i~~-~g~~vG~k~~l~f~~~~~~~~~~~~t~W~M~EY~l~ 135 (144)
+++|+||++|+.++|.+ ++.+||+|++|+||.++.+++ .+|+|+||||+|.
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~--~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNG--KKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS---EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCCCC--CcCCeEEEEEEeC
Confidence 99999999999999999 699999999999998877666 8999999999984
No 2
>PHA00692 hypothetical protein
Probab=60.20 E-value=3.4 Score=25.41 Aligned_cols=9 Identities=22% Similarity=0.696 Sum_probs=7.5
Q ss_pred CCCCCceEc
Q 032247 4 HMGQGYKFQ 12 (144)
Q Consensus 4 ~lp~G~rF~ 12 (144)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 579999995
No 3
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=39.92 E-value=32 Score=26.38 Aligned_cols=61 Identities=15% Similarity=0.195 Sum_probs=33.7
Q ss_pred CCCCceEcCCHH-HHHHHHhhhhCCCCCCCCCeeccCCCCCCCCCCccccccCCCCCCeEEEE
Q 032247 5 MGQGYKFQPSDE-LIVSLLKEKRLDPHFLYGPIKDIGHICNLEPGDLATESETDSEDRACYFF 66 (144)
Q Consensus 5 lp~G~rF~Ptde-Li~~YL~~k~~g~~l~~~~I~~~~Dvy~~~P~~L~~~~~~~~~~~~~yFF 66 (144)
.--+|||.|+|. -+...--....+..+-+....+. +-|+-+=|+.-......++...||=.
T Consensus 109 ~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~-~~~dgee~~mea~d~~~gDs~~~~t~ 170 (216)
T KOG3238|consen 109 PITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDE-DDYDGEEYDMEAHDAGQGDSPNSYTY 170 (216)
T ss_pred ccccceecCCchhHHHHHHHHHHhhhhcCCCccccc-cccccchhhhhhhhccCCCCcccccc
Confidence 345899999999 65553333444444433335555 66666666665443333344444433
No 4
>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=31.74 E-value=37 Score=15.39 Aligned_cols=8 Identities=25% Similarity=0.708 Sum_probs=6.3
Q ss_pred CCeEEEEe
Q 032247 60 DRACYFFY 67 (144)
Q Consensus 60 ~~~~yFF~ 67 (144)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47899994
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=27.61 E-value=79 Score=23.64 Aligned_cols=27 Identities=15% Similarity=0.474 Sum_probs=18.4
Q ss_pred ceeEeecCC-ceEeeCCcEEEEEEEEEE
Q 032247 86 GHWKITSED-SQIEASNGLIGTKKFLTF 112 (144)
Q Consensus 86 G~W~~~g~~-~~i~~~g~~vG~k~~l~f 112 (144)
--|.++|-. +.|..+|+++|+...|..
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 459999876 677778999999998875
No 6
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=26.00 E-value=94 Score=15.95 Aligned_cols=19 Identities=16% Similarity=0.232 Sum_probs=14.4
Q ss_pred CHH-HHHHHHhhhhCCCCCC
Q 032247 14 SDE-LIVSLLKEKRLDPHFL 32 (144)
Q Consensus 14 tde-Li~~YL~~k~~g~~l~ 32 (144)
+.. ||.+|+.-|+.....+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 445 9999999999865443
No 7
>COG3908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.49 E-value=46 Score=21.11 Aligned_cols=20 Identities=20% Similarity=0.511 Sum_probs=14.7
Q ss_pred CCeEEEEEEeCCCCCeeecC
Q 032247 125 TDWVMHEYHVKDDPSYEVCA 144 (144)
Q Consensus 125 t~W~M~EY~l~~~~~~vlC~ 144 (144)
-..+--.|.+.+..++|+|+
T Consensus 15 iryldgdf~vv~~GsfV~CA 34 (77)
T COG3908 15 IRYLDGDFQVVSPGSFVLCA 34 (77)
T ss_pred EEEecCceEEEcCCcEEEEE
Confidence 34555567888888899996
No 8
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=19.74 E-value=40 Score=24.72 Aligned_cols=13 Identities=15% Similarity=0.457 Sum_probs=11.0
Q ss_pred CCCCCceEcCCHH
Q 032247 4 HMGQGYKFQPSDE 16 (144)
Q Consensus 4 ~lp~G~rF~Ptde 16 (144)
++-|+|.++|+|.
T Consensus 84 P~lp~F~ynP~D~ 96 (156)
T PF10107_consen 84 PFLPEFPYNPKDA 96 (156)
T ss_pred hccCCCCCChhhh
Confidence 3569999999997
No 9
>PRK14390 hypothetical protein; Provisional
Probab=18.79 E-value=53 Score=20.37 Aligned_cols=12 Identities=33% Similarity=0.587 Sum_probs=10.1
Q ss_pred CCCCceEcCCHH
Q 032247 5 MGQGYKFQPSDE 16 (144)
Q Consensus 5 lp~G~rF~Ptde 16 (144)
+|+-+||.||=-
T Consensus 13 ~~~~CRf~PTCS 24 (63)
T PRK14390 13 FGPRCRFIPSCS 24 (63)
T ss_pred CCCCCCcCccHH
Confidence 688999999954
No 10
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=18.26 E-value=46 Score=24.52 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=11.5
Q ss_pred CCCCCceEcCCHH-HH
Q 032247 4 HMGQGYKFQPSDE-LI 18 (144)
Q Consensus 4 ~lp~G~rF~Ptde-Li 18 (144)
++-|+|+|+|.|. -|
T Consensus 97 Pffp~f~ynPkD~RfI 112 (175)
T COG4741 97 PFFPEFKYNPKDARFI 112 (175)
T ss_pred ccccCCCcCCccceee
Confidence 3557999999997 54
Done!