Query 017665
Match_columns 368
No_of_seqs 221 out of 971
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 02:22:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017665.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017665hhsearch_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 2.2E-44 4.7E-49 308.9 6.8 128 11-142 1-129 (129)
2 PHA00692 hypothetical protein 24.5 28 0.0006 27.3 0.3 10 9-18 35-44 (74)
3 cd00490 Met_repressor_MetJ Met 20.9 88 0.0019 26.4 2.5 39 18-60 50-88 (103)
4 PRK05264 transcriptional repre 19.2 93 0.002 26.4 2.3 39 18-60 51-89 (105)
5 COG3060 MetJ Transcriptional r 16.5 87 0.0019 26.3 1.5 39 18-60 51-89 (105)
6 PF01340 MetJ: Met Apo-repress 16.3 1.2E+02 0.0026 25.7 2.3 39 18-60 50-88 (104)
7 smart00265 BH4 BH4 Bcl-2 homol 16.1 1.5E+02 0.0034 19.6 2.3 20 20-39 4-23 (27)
8 PF07960 CBP4: CBP4; InterPro 14.1 91 0.002 27.8 1.2 11 18-28 30-40 (128)
9 PF01473 CW_binding_1: Putativ 10.6 1.7E+02 0.0037 17.0 1.2 8 64-71 7-14 (19)
10 PF07491 PPI_Ypi1: Protein pho 10.4 2.5E+02 0.0055 22.0 2.4 16 165-180 36-51 (60)
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=2.2e-44 Score=308.94 Aligned_cols=128 Identities=60% Similarity=1.174 Sum_probs=97.5
Q ss_pred CCCCceeCCCHHHHHHHHHHHhHhCCCCCc-ceeeeccCCCCCCCCccccccCCCceEEEeccCCCCCCCCCCCcccCCC
Q 017665 11 LPPGFRFHPTDEELILHYLKKKVASMPFPV-SIIADVDIYKFDPWDLPAKAAFGEKEWYFFSPRDRKYPNGARPNRAAAS 89 (368)
Q Consensus 11 LPpGfRF~PTDEELI~~YL~~Ki~g~plp~-~iI~evDVY~~dPWdLP~k~~~ge~eWYFFspr~rKy~nG~R~nRatg~ 89 (368)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||.+|||+|++....++.+||||+++.+++.+|.|++|++++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~ 80 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGG 80 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETT
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccc
Confidence 899999999999999999999999999988 7899999999999999965445678999999999999999999999999
Q ss_pred CeEEeeccceeEEecccCCceeeEEEEEEEEEeeCCCCCCCccCeEEEEEEeC
Q 017665 90 GYWKATGTDKIILATSVGAHQENIGVKKALVFYKGRPPKGVKTNWIMHEYRLA 142 (368)
Q Consensus 90 GyWKatG~dk~I~~~~~GG~g~~VG~KKtLvFY~Gr~pkG~KT~WvMhEYrL~ 142 (368)
|+||++|+++.|... ++++||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~----~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDP----GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-----TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccc----cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999985 3689999999999999888999999999999984
No 2
>PHA00692 hypothetical protein
Probab=24.51 E-value=28 Score=27.28 Aligned_cols=10 Identities=60% Similarity=1.268 Sum_probs=8.4
Q ss_pred CCCCCCceeC
Q 017665 9 SALPPGFRFH 18 (368)
Q Consensus 9 ~~LPpGfRF~ 18 (368)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4689999995
No 3
>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=20.94 E-value=88 Score=26.43 Aligned_cols=39 Identities=26% Similarity=0.415 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhHhCCCCCcceeeeccCCCCCCCCccccc
Q 017665 18 HPTDEELILHYLKKKVASMPFPVSIIADVDIYKFDPWDLPAKA 60 (368)
Q Consensus 18 ~PTDEELI~~YL~~Ki~g~plp~~iI~evDVY~~dPWdLP~k~ 60 (368)
|-|.-||++.-...-..|+|+|.+ .|+-+..|.++|+.+
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D----~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDD----ADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCcccccHHH
Confidence 567788888666678889999974 789999999999865
No 4
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=19.25 E-value=93 Score=26.44 Aligned_cols=39 Identities=26% Similarity=0.398 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhHhCCCCCcceeeeccCCCCCCCCccccc
Q 017665 18 HPTDEELILHYLKKKVASMPFPVSIIADVDIYKFDPWDLPAKA 60 (368)
Q Consensus 18 ~PTDEELI~~YL~~Ki~g~plp~~iI~evDVY~~dPWdLP~k~ 60 (368)
|-|.-||++.-...-..|+|+|.+ .|+-+..|.++|+.+
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~D----~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPDD----EDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCCh----hhhhhcCcccchHHH
Confidence 567788888666678889999974 789999999999765
No 5
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=16.45 E-value=87 Score=26.31 Aligned_cols=39 Identities=26% Similarity=0.440 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhHhCCCCCcceeeeccCCCCCCCCccccc
Q 017665 18 HPTDEELILHYLKKKVASMPFPVSIIADVDIYKFDPWDLPAKA 60 (368)
Q Consensus 18 ~PTDEELI~~YL~~Ki~g~plp~~iI~evDVY~~dPWdLP~k~ 60 (368)
|-|..||++.-...-..|+|+|.+ .|+-+.-|.++|+.+
T Consensus 51 hatnsellceaflhaftgqplptd----~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPTD----ADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCCc----HHHHHhccccchHHH
Confidence 567788888666677889999964 799999999999876
No 6
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=16.29 E-value=1.2e+02 Score=25.73 Aligned_cols=39 Identities=31% Similarity=0.504 Sum_probs=25.0
Q ss_pred CCCHHHHHHHHHHHhHhCCCCCcceeeeccCCCCCCCCccccc
Q 017665 18 HPTDEELILHYLKKKVASMPFPVSIIADVDIYKFDPWDLPAKA 60 (368)
Q Consensus 18 ~PTDEELI~~YL~~Ki~g~plp~~iI~evDVY~~dPWdLP~k~ 60 (368)
|-|.-||++.-...-..|+|+|.+ .|+-+..|.++|+.+
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~D----~dl~kd~~d~ip~~~ 88 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPTD----DDLRKDRPDEIPAEA 88 (104)
T ss_dssp S-SHHHHHHHHHHHHHH------T----TGGGSTSGSSS-HHH
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCCccchHHH
Confidence 567888888666678889999974 789999999999865
No 7
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=16.11 E-value=1.5e+02 Score=19.61 Aligned_cols=20 Identities=20% Similarity=0.504 Sum_probs=15.7
Q ss_pred CHHHHHHHHHHHhHhCCCCC
Q 017665 20 TDEELILHYLKKKVASMPFP 39 (368)
Q Consensus 20 TDEELI~~YL~~Ki~g~plp 39 (368)
+-.|||++|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999755443
No 8
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=14.10 E-value=91 Score=27.78 Aligned_cols=11 Identities=55% Similarity=0.939 Sum_probs=9.4
Q ss_pred CCCHHHHHHHH
Q 017665 18 HPTDEELILHY 28 (368)
Q Consensus 18 ~PTDEELI~~Y 28 (368)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 9
>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=10.59 E-value=1.7e+02 Score=17.01 Aligned_cols=8 Identities=38% Similarity=1.468 Sum_probs=6.2
Q ss_pred CceEEEec
Q 017665 64 EKEWYFFS 71 (368)
Q Consensus 64 e~eWYFFs 71 (368)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 36799995
No 10
>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=10.41 E-value=2.5e+02 Score=21.95 Aligned_cols=16 Identities=25% Similarity=0.287 Sum_probs=12.1
Q ss_pred eEEEEEEEcCCCCCCC
Q 017665 165 WVLCRIYRKSHVSLPT 180 (368)
Q Consensus 165 ~VLCRIykK~~~~~~s 180 (368)
--+|-||.|++....+
T Consensus 36 SK~CCIyhk~~~~~es 51 (60)
T PF07491_consen 36 SKCCCIYHKPRAFDES 51 (60)
T ss_pred CceeeeecCCCCCCCC
Confidence 4589999999876543
Done!