Query 037150
Match_columns 346
No_of_seqs 163 out of 920
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 09:09:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037150.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037150hhsearch_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 8.7E-30 1.9E-34 216.8 6.8 104 1-107 24-129 (129)
2 PF00418 Tubulin-binding: Tau 21.9 46 0.001 22.5 0.9 13 266-278 14-26 (31)
3 PF05865 Cypo_polyhedrin: Cypo 14.1 1.8E+02 0.0039 27.1 3.1 27 60-86 141-168 (248)
4 KOG4286 Dystrophin-like protei 13.0 40 0.00088 37.7 -1.6 56 75-136 612-679 (966)
5 PF08653 DASH_Dam1: DASH compl 10.4 1.4E+02 0.003 22.9 1.0 26 289-314 8-33 (58)
6 PF01473 CW_binding_1: Putativ 9.6 2.1E+02 0.0045 16.4 1.3 8 32-39 7-14 (19)
7 COG3100 Uncharacterized protei 8.2 2.2E+02 0.0048 24.1 1.5 14 123-136 9-22 (103)
8 PRK10154 hypothetical protein; 5.5 6.4E+02 0.014 22.4 2.9 23 79-102 78-100 (134)
9 PF15102 TMEM154: TMEM154 prot 5.5 1.9E+02 0.0042 26.0 -0.2 19 125-143 75-93 (146)
10 PF06645 SPC12: Microsomal sig 5.1 3.4E+02 0.0073 21.5 1.0 22 319-343 53-74 (76)
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=99.96 E-value=8.7e-30 Score=216.76 Aligned_cols=104 Identities=46% Similarity=0.848 Sum_probs=79.0
Q ss_pred CCCCCCC-CceeecCCCCCCccchhhHhhhCCCceEEEEeecCccCCCCCCCceeccCCCceeeeecCCceeee-CCeee
Q 037150 1 MNEPLPP-NRIMDVQLYKFSPAQLEVMYKKRREKEMFFFTQRDRKHQNGSRPNRVTGDSSGFWKATSGDKEVKF-NGEII 78 (346)
Q Consensus 1 mG~PLP~-~iI~evDVY~~ePWdLP~~~~~~gd~eWYFFspr~rKy~nG~R~~Ratg~ggGyWKatG~~k~I~~-~g~vI 78 (346)
+|.|+|. .+|+++|||++|||+|++. ...++++||||+++.+++.++.|++|++ ++|+||++|+.++|.. ++.+|
T Consensus 24 ~g~~~~~~~~i~~~Diy~~~P~~L~~~-~~~~~~~~yFF~~~~~~~~~~~r~~R~~--~~G~Wk~~g~~~~i~~~~g~~i 100 (129)
T PF02365_consen 24 LGEPLPCEDVIHDVDIYSAHPWELPAK-FKGGDEEWYFFSPRKKKYPNGGRPNRVT--GGGYWKSTGKEKPIKDPGGKVI 100 (129)
T ss_dssp TT-HHCS-CHSEE--GGGS-GGGCHHH-SSS-SSEEEEEEE----------S-EEE--TTEEEEEECEEEEEEE-TTCEE
T ss_pred cCCCCCcccceeecccCccChHHhhhh-ccCCCceEEEEEecccccCCcccccccc--cceEEeecccccccccccceee
Confidence 4677888 7999999999999999964 4456789999999999999999999999 9999999999999998 69999
Q ss_pred EEEEEEeeeeccCCCCCccCeEEEEeeeC
Q 037150 79 GFKKTLAFYKRTSNSTEKTNWIMHEFRAE 107 (346)
Q Consensus 79 G~KKtLvFY~Gr~p~g~KT~WvMhEY~l~ 107 (346)
|+|++|+||.++.+++.+|+|+||||+|.
T Consensus 101 G~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 101 GFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999888999999999999984
No 2
>PF00418 Tubulin-binding: Tau and MAP protein, tubulin-binding repeat; InterPro: IPR001084 Microtubules consist of tubulins as well as a group of additional proteins collectively known as the Microtubule Associated Proteins (MAP). MAP's have been classified into two classes: high molecular weight MAP's and Tau protein. The Tau proteins promote microtubule assembly and stabilise microtubules. The C-terminal region of these proteins contains three or four tandem repeats of a conserved domain of about thirty amino acid residues which is implicated in tubulin-binding and which seems to have a stiffening effect on microtubules.; GO: 0007026 negative regulation of microtubule depolymerization
Probab=21.93 E-value=46 Score=22.52 Aligned_cols=13 Identities=38% Similarity=0.677 Sum_probs=11.1
Q ss_pred ccCCCCccccccc
Q 037150 266 YANASSLDNMHHQ 278 (346)
Q Consensus 266 ~~~~~~~~~~~~~ 278 (346)
-++|+|||||.|.
T Consensus 14 ~SK~GS~~N~~H~ 26 (31)
T PF00418_consen 14 QSKCGSLDNIKHK 26 (31)
T ss_pred ccccccccccccc
Confidence 3799999999884
No 3
>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=14.08 E-value=1.8e+02 Score=27.10 Aligned_cols=27 Identities=26% Similarity=0.618 Sum_probs=18.0
Q ss_pred ceeeeec-CCceeeeCCeeeEEEEEEee
Q 037150 60 GFWKATS-GDKEVKFNGEIIGFKKTLAF 86 (346)
Q Consensus 60 GyWKatG-~~k~I~~~g~vIG~KKtLvF 86 (346)
--|.+|| +-|.|..+|++||+...|..
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 4599998 66888889999999887754
No 4
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=13.02 E-value=40 Score=37.69 Aligned_cols=56 Identities=20% Similarity=0.288 Sum_probs=41.5
Q ss_pred CeeeEEEE-EEe----------eeeccCCCCCccCeEEEEeeeCCCCCCCCCCCCCCCc-ceEEEEEEEcCCCC
Q 037150 75 GEIIGFKK-TLA----------FYKRTSNSTEKTNWIMHEFRAEDNPPPSKKHGIDMKL-DWVLCRIYHRGSKS 136 (346)
Q Consensus 75 g~vIG~KK-tLv----------FY~Gr~p~g~KT~WvMhEY~l~~~~~~~~~~~~~~~~-d~VLCRIykK~~~~ 136 (346)
..|||+|- +|+ |..|++.+|.|++.-|.||.....+... +++ .-|||--|+.++.-
T Consensus 612 ~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tts~~d------~rdfak~L~nkfr~~~~~ 679 (966)
T KOG4286|consen 612 CPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTTSGED------VRDFAKVLKNKFRTKRYF 679 (966)
T ss_pred CccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCCChhh------HHHHHHHHHhhhccchhh
Confidence 56788863 344 5679999999999999999998876532 344 55888888866543
No 5
>PF08653 DASH_Dam1: DASH complex subunit Dam1; InterPro: IPR013962 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=10.38 E-value=1.4e+02 Score=22.88 Aligned_cols=26 Identities=35% Similarity=0.450 Sum_probs=21.8
Q ss_pred cccCcchhhhHHHHHHHHHHHhhhcC
Q 037150 289 AQPSNSMIAMDAELQAFAVITESLLS 314 (346)
Q Consensus 289 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 314 (346)
.+.+.||.+++.+..+.+.|.|+|-.
T Consensus 8 ~eL~D~~~~L~~n~~~L~~ihesL~~ 33 (58)
T PF08653_consen 8 AELSDSMETLDKNMEQLNQIHESLSD 33 (58)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567999999999999999998753
No 6
>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=9.55 E-value=2.1e+02 Score=16.44 Aligned_cols=8 Identities=13% Similarity=0.704 Sum_probs=6.1
Q ss_pred CceEEEEe
Q 037150 32 EKEMFFFT 39 (346)
Q Consensus 32 d~eWYFFs 39 (346)
+..||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 46899994
No 7
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=8.20 E-value=2.2e+02 Score=24.08 Aligned_cols=14 Identities=36% Similarity=0.669 Sum_probs=11.4
Q ss_pred ceEEEEEEEcCCCC
Q 037150 123 DWVLCRIYHRGSKS 136 (346)
Q Consensus 123 d~VLCRIykK~~~~ 136 (346)
--.||-||+++++.
T Consensus 9 ~~mlCaIYkS~kk~ 22 (103)
T COG3100 9 KSMLCAIYKSPKKD 22 (103)
T ss_pred eeeeeeeeecCcCC
Confidence 45899999998775
No 8
>PRK10154 hypothetical protein; Provisional
Probab=5.47 E-value=6.4e+02 Score=22.42 Aligned_cols=23 Identities=17% Similarity=0.333 Sum_probs=16.3
Q ss_pred EEEEEEeeeeccCCCCCccCeEEE
Q 037150 79 GFKKTLAFYKRTSNSTEKTNWIMH 102 (346)
Q Consensus 79 G~KKtLvFY~Gr~p~g~KT~WvMh 102 (346)
|..++|.||..= .++..|+|+--
T Consensus 78 g~s~tl~f~~~l-k~~q~T~W~~~ 100 (134)
T PRK10154 78 SASQSLNIPSEI-KEGQTTDWINI 100 (134)
T ss_pred CCceEEecchhh-ccCCccccEEc
Confidence 445888888643 46889999854
No 9
>PF15102 TMEM154: TMEM154 protein family
Probab=5.46 E-value=1.9e+02 Score=26.03 Aligned_cols=19 Identities=21% Similarity=0.405 Sum_probs=10.9
Q ss_pred EEEEEEEcCCCCCccccCC
Q 037150 125 VLCRIYHRGSKSKRADQAS 143 (346)
Q Consensus 125 VLCRIykK~~~~kk~~~~~ 143 (346)
|+|-|++.+|++.|.+..+
T Consensus 75 vV~lv~~~kRkr~K~~~ss 93 (146)
T PF15102_consen 75 VVCLVIYYKRKRTKQEPSS 93 (146)
T ss_pred HHHheeEEeecccCCCCcc
Confidence 6677776665555544333
No 10
>PF06645 SPC12: Microsomal signal peptidase 12 kDa subunit (SPC12); InterPro: IPR009542 This family consists of several microsomal signal peptidase 12 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 12 kDa subunit (SPC12).; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0005787 signal peptidase complex, 0016021 integral to membrane
Probab=5.12 E-value=3.4e+02 Score=21.49 Aligned_cols=22 Identities=36% Similarity=0.877 Sum_probs=17.8
Q ss_pred CcccccccccccCCCCCCCCccccc
Q 037150 319 ASVYPFKSSYARNDPLWMPTLPEFQ 343 (346)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~~~~~~~~ 343 (346)
.-+||+ |.||...|.+..++-+
T Consensus 53 vP~Wp~---y~r~p~~W~~~~~~~~ 74 (76)
T PF06645_consen 53 VPPWPF---YNRHPLKWLPPKPEKE 74 (76)
T ss_pred eCCcHh---hcCCcccCCCCCcccc
Confidence 347998 8899999999887644
Done!