Query 047639
Match_columns 260
No_of_seqs 167 out of 863
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 13:11:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047639.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047639hhsearch_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 9.4E-40 2E-44 266.4 8.3 119 4-133 1-129 (129)
2 PHA00692 hypothetical protein 28.6 21 0.00046 25.7 0.3 9 3-11 36-44 (74)
3 PF07131 DUF1382: Protein of u 22.1 92 0.002 22.4 2.5 20 6-25 22-48 (61)
4 PF02375 JmjN: jmjN domain; I 21.7 80 0.0017 20.0 1.9 15 9-23 2-19 (34)
5 PF08672 APC2: Anaphase promot 17.8 72 0.0016 22.7 1.2 23 9-31 30-52 (60)
6 PF13822 ACC_epsilon: Acyl-CoA 16.7 70 0.0015 22.8 0.9 17 11-27 10-29 (62)
7 PF01473 CW_binding_1: Putativ 16.1 1E+02 0.0022 16.4 1.3 8 55-62 7-14 (19)
8 cd00490 Met_repressor_MetJ Met 15.6 1.5E+02 0.0032 23.2 2.5 37 11-53 50-87 (103)
9 COG3060 MetJ Transcriptional r 14.4 1.1E+02 0.0025 23.6 1.6 37 12-54 52-89 (105)
10 PRK05264 transcriptional repre 14.2 1.5E+02 0.0033 23.2 2.3 37 11-53 51-88 (105)
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=9.4e-40 Score=266.40 Aligned_cols=119 Identities=39% Similarity=0.727 Sum_probs=91.9
Q ss_pred CCCCceEcCCHHHH-HHHHHHHHcCCCCCCCcceeeeccCCCCCCcccCCC---CCCeEEEEEecc------CCCccccC
Q 047639 4 VPKGFRFNPTDEEL-IQILESKVSGQQMPLHFSFIVERNLYELEPQQLQSL---PENERYCYCMRE------NDSREVSG 73 (260)
Q Consensus 4 LPpGfRF~PTDeEL-~~YL~~Ki~g~plp~~~~~I~e~Dvy~~~Pw~Lp~~---~~~ewYFFs~~~------~r~~R~~~ 73 (260)
|||||||+|||+|| .+||++|+.|.+++. ..+|+++|||++|||+|+.. .+++||||++++ +|.+|+++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~-~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~ 79 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPC-EDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTG 79 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS--CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEET
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCc-ccceeecccCccChHHhhhhccCCCceEEEEEecccccCCccccccccc
Confidence 89999999999999 899999999999884 48899999999999999932 278999999997 45688999
Q ss_pred CceEEeecCceEEEEcCCCCCcceeeEEEeeeeeecccCCCCCCCCCcccCeeEeEeeec
Q 047639 74 RGWWKATSHVKKIYATNNNGSCADVIGYKRPLTFHKFKNNGRNRSNAIKTNWIMHEYTLH 133 (260)
Q Consensus 74 ~G~Wk~~G~~k~I~~~~~~g~~~~viG~Kk~l~Fy~~~~~~~~~~~~~kT~WvMhEY~l~ 133 (260)
+|+||++|+.+.|... + +.+||+|++|+||.++. +++.+|+|+||||+|.
T Consensus 80 ~G~Wk~~g~~~~i~~~-~----g~~iG~k~~l~f~~~~~-----~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 80 GGYWKSTGKEKPIKDP-G----GKVIGFKKTLVFYSGKS-----PNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TEEEEEECEEEEEEE--T----TCEEEEEEEEEEEESST-----TS-EEEEEEEEEEEE-
T ss_pred ceEEeecccccccccc-c----ceeeeeEEEEEEEeccC-----CCCCcCCeEEEEEEeC
Confidence 9999999999999985 3 38999999999998766 7889999999999984
No 2
>PHA00692 hypothetical protein
Probab=28.61 E-value=21 Score=25.69 Aligned_cols=9 Identities=56% Similarity=1.095 Sum_probs=7.1
Q ss_pred CCCCCceEc
Q 047639 3 MVPKGFRFN 11 (260)
Q Consensus 3 ~LPpGfRF~ 11 (260)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 578999984
No 3
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=22.13 E-value=92 Score=22.43 Aligned_cols=20 Identities=50% Similarity=0.748 Sum_probs=13.1
Q ss_pred CCceEcC----CHHHH---HHHHHHHH
Q 047639 6 KGFRFNP----TDEEL---IQILESKV 25 (260)
Q Consensus 6 pGfRF~P----TDeEL---~~YL~~Ki 25 (260)
.|+||.| ||+|+ ..-|.+|+
T Consensus 22 ~GIRFVpiPv~~dee~~~L~s~~~~kL 48 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHTLSSQLSQKL 48 (61)
T ss_pred cCceeeccccccHHHHHHHHHHHHHHH
Confidence 4999999 67776 33444443
No 4
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=21.73 E-value=80 Score=20.02 Aligned_cols=15 Identities=47% Similarity=0.665 Sum_probs=8.9
Q ss_pred eEcCCHHHH---HHHHHH
Q 047639 9 RFNPTDEEL---IQILES 23 (260)
Q Consensus 9 RF~PTDeEL---~~YL~~ 23 (260)
-|+||.||. ..||..
T Consensus 2 vf~Pt~eEF~dp~~yi~~ 19 (34)
T PF02375_consen 2 VFYPTMEEFKDPIKYISS 19 (34)
T ss_dssp EE---HHHHS-HHHHHHH
T ss_pred cccCCHHHHhCHHHHHHH
Confidence 389999999 666665
No 5
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=17.78 E-value=72 Score=22.68 Aligned_cols=23 Identities=22% Similarity=0.338 Sum_probs=17.3
Q ss_pred eEcCCHHHHHHHHHHHHcCCCCC
Q 047639 9 RFNPTDEELIQILESKVSGQQMP 31 (260)
Q Consensus 9 RF~PTDeEL~~YL~~Ki~g~plp 31 (260)
.|..|.+||..||..++....+.
T Consensus 30 ~~~~s~~eL~~fL~~lv~e~~L~ 52 (60)
T PF08672_consen 30 GYDISLEELQEFLDRLVEEGKLE 52 (60)
T ss_dssp -TT--HHHHHHHHHHHHHTTSEE
T ss_pred CCCCCHHHHHHHHHHHHHCCcEE
Confidence 45678999999999999987764
No 6
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=16.72 E-value=70 Score=22.80 Aligned_cols=17 Identities=47% Similarity=0.815 Sum_probs=10.9
Q ss_pred cCCHHHH---HHHHHHHHcC
Q 047639 11 NPTDEEL---IQILESKVSG 27 (260)
Q Consensus 11 ~PTDeEL---~~YL~~Ki~g 27 (260)
+|||||| +--|.-....
T Consensus 10 nPt~eElAAL~aVlaa~~a~ 29 (62)
T PF13822_consen 10 NPTDEELAALTAVLAARAAA 29 (62)
T ss_pred CCCHHHHHHHHHHHHHHhcc
Confidence 7999999 4444444433
No 7
>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=16.08 E-value=1e+02 Score=16.39 Aligned_cols=8 Identities=13% Similarity=0.410 Sum_probs=5.9
Q ss_pred CCeEEEEE
Q 047639 55 ENERYCYC 62 (260)
Q Consensus 55 ~~ewYFFs 62 (260)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47799983
No 8
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=15.63 E-value=1.5e+02 Score=23.19 Aligned_cols=37 Identities=19% Similarity=0.366 Sum_probs=27.3
Q ss_pred cCCHHHH-HHHHHHHHcCCCCCCCcceeeeccCCCCCCcccCCC
Q 047639 11 NPTDEEL-IQILESKVSGQQMPLHFSFIVERNLYELEPQQLQSL 53 (260)
Q Consensus 11 ~PTDeEL-~~YL~~Ki~g~plp~~~~~I~e~Dvy~~~Pw~Lp~~ 53 (260)
+-|..|| +.-...-..|+||| .+.|+-...|.++|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP------~D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLP------DDADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCC------ChhhhhhcCcccccHH
Confidence 3466788 44444567899999 5778888889888864
No 9
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=14.44 E-value=1.1e+02 Score=23.59 Aligned_cols=37 Identities=19% Similarity=0.384 Sum_probs=27.6
Q ss_pred CCHHHH-HHHHHHHHcCCCCCCCcceeeeccCCCCCCcccCCCC
Q 047639 12 PTDEEL-IQILESKVSGQQMPLHFSFIVERNLYELEPQQLQSLP 54 (260)
Q Consensus 12 PTDeEL-~~YL~~Ki~g~plp~~~~~I~e~Dvy~~~Pw~Lp~~~ 54 (260)
-|..|| +.-...-..|+||| .+.|+....|.++|...
T Consensus 52 atnsellceaflhaftgqplp------td~dl~ker~deipe~a 89 (105)
T COG3060 52 ATNSELLCEAFLHAFTGQPLP------TDADLRKERSDEIPEAA 89 (105)
T ss_pred hhhHHHHHHHHHHHHcCCCCC------CcHHHHHhccccchHHH
Confidence 466777 54445567899999 57899888888888643
No 10
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=14.18 E-value=1.5e+02 Score=23.19 Aligned_cols=37 Identities=19% Similarity=0.375 Sum_probs=27.2
Q ss_pred cCCHHHH-HHHHHHHHcCCCCCCCcceeeeccCCCCCCcccCCC
Q 047639 11 NPTDEEL-IQILESKVSGQQMPLHFSFIVERNLYELEPQQLQSL 53 (260)
Q Consensus 11 ~PTDeEL-~~YL~~Ki~g~plp~~~~~I~e~Dvy~~~Pw~Lp~~ 53 (260)
+-|..|| +.-...-..|+||| .+.|+-...|.++|..
T Consensus 51 HATNSELLCEAFLHA~TGQPLP------~D~Dl~Kd~~d~ip~~ 88 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLP------DDEDLRKERSDEIPEA 88 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCC------ChhhhhhcCcccchHH
Confidence 3466788 44444567899999 5778988889888853
Done!