Query 029281
Match_columns 196
No_of_seqs 131 out of 872
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 10:23:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029281hhsearch_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 7.2E-45 1.6E-49 280.1 6.6 126 15-143 1-129 (129)
2 cd00490 Met_repressor_MetJ Met 50.7 19 0.00042 26.1 2.9 38 22-63 50-87 (103)
3 PF01340 MetJ: Met Apo-repress 48.7 20 0.00042 26.1 2.7 38 22-63 50-87 (104)
4 PRK05264 transcriptional repre 46.7 22 0.00047 26.0 2.7 38 22-63 51-88 (105)
5 PHA00692 hypothetical protein 42.8 9.8 0.00021 25.5 0.4 11 13-23 35-45 (74)
6 COG3060 MetJ Transcriptional r 32.8 34 0.00074 24.7 1.9 38 22-63 51-88 (105)
7 PF06404 PSK: Phytosulfokine p 32.3 16 0.00035 25.9 0.2 14 182-195 67-80 (81)
8 KOG1334 WD40 repeat protein [G 29.5 77 0.0017 30.0 4.1 98 27-125 304-434 (559)
9 PF07960 CBP4: CBP4; InterPro 25.3 37 0.00079 26.3 1.0 11 22-32 30-40 (128)
10 PF13822 ACC_epsilon: Acyl-CoA 25.1 38 0.00082 22.6 1.0 9 22-30 10-18 (62)
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=7.2e-45 Score=280.06 Aligned_cols=126 Identities=44% Similarity=0.891 Sum_probs=96.2
Q ss_pred CCCCeeeCCChHHHHHHHHHHhhcCCCCCC-CcccccCCCCCCCCCCCCc--CCCCeEEEEeccccccccCCCCcccccc
Q 029281 15 LPIGYRFRPTDEELVVHYLKRKVFGLPLPA-SIIPELDVFQSHPLGLPGD--MKEKKRYFFSNIRNESAIDNDGKCKIAA 91 (196)
Q Consensus 15 LppG~rF~PTDeELv~~YL~~k~~g~~l~~-~~I~~~Dvy~~~Pw~Lp~~--~~~~~~yFFs~~~~~~~~~~g~R~~R~~ 91 (196)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||++|||+|+.. .++++||||++ ++.++.++.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~--~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSP--RKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE------------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEe--cccccCCcccccccc
Confidence 899999999999999999999999999888 8999999999999999932 45689999999 666677889999999
Q ss_pred CCceeeecCCceeeEecCCCeEEEEEEEeeeecccCCCCCccCeEEEEEEeC
Q 029281 92 GSGYWKPVGKNRQILASGTKQVVGIRKTLIFCEGKRGHETKTQWVMHQYHLV 143 (196)
Q Consensus 92 g~G~Wk~~g~~~~I~~~~~g~~vG~kk~l~F~~g~~~~~~kT~W~M~EY~l~ 143 (196)
++|+||++|+.++|.. .++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~-~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKD-PGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cceEEeeccccccccc-ccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999987 48999999999999998888899999999999984
No 2
>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=50.71 E-value=19 Score=26.13 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=31.3
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCCcccccCCCCCCCCCCCCc
Q 029281 22 RPTDEELVVHYLKRKVFGLPLPASIIPELDVFQSHPLGLPGD 63 (196)
Q Consensus 22 ~PTDeELv~~YL~~k~~g~~l~~~~I~~~Dvy~~~Pw~Lp~~ 63 (196)
|-|..||++.-..--..|+|||.+ .|+-...|.++|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D----~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDD----ADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCcccccHH
Confidence 568889988877788899999985 48888888888865
No 3
>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=48.65 E-value=20 Score=26.13 Aligned_cols=38 Identities=26% Similarity=0.483 Sum_probs=24.2
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCCcccccCCCCCCCCCCCCc
Q 029281 22 RPTDEELVVHYLKRKVFGLPLPASIIPELDVFQSHPLGLPGD 63 (196)
Q Consensus 22 ~PTDeELv~~YL~~k~~g~~l~~~~I~~~Dvy~~~Pw~Lp~~ 63 (196)
|-|..||++.-..--..|+|||.+ .|+-...|.++|..
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~D----~dl~kd~~d~ip~~ 87 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPTD----DDLRKDRPDEIPAE 87 (104)
T ss_dssp S-SHHHHHHHHHHHHHH------T----TGGGSTSGSSS-HH
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCCccchHH
Confidence 578889998877788899999985 48888888888865
No 4
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=46.69 E-value=22 Score=26.01 Aligned_cols=38 Identities=24% Similarity=0.383 Sum_probs=31.1
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCCcccccCCCCCCCCCCCCc
Q 029281 22 RPTDEELVVHYLKRKVFGLPLPASIIPELDVFQSHPLGLPGD 63 (196)
Q Consensus 22 ~PTDeELv~~YL~~k~~g~~l~~~~I~~~Dvy~~~Pw~Lp~~ 63 (196)
|-|..||++.-..--..|+|||.+ .|+-...|.++|..
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~D----~Dl~Kd~~d~ip~~ 88 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPDD----EDLRKERSDEIPEA 88 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCCh----hhhhhcCcccchHH
Confidence 568889988877788899999985 48888888888854
No 5
>PHA00692 hypothetical protein
Probab=42.75 E-value=9.8 Score=25.53 Aligned_cols=11 Identities=36% Similarity=0.872 Sum_probs=8.8
Q ss_pred cCCCCCeeeCC
Q 029281 13 LKLPIGYRFRP 23 (196)
Q Consensus 13 ~~LppG~rF~P 23 (196)
++.||||||--
T Consensus 35 veyppgfrfgg 45 (74)
T PHA00692 35 VEYPPGFRFGG 45 (74)
T ss_pred EecCCCccccc
Confidence 56899999963
No 6
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=32.80 E-value=34 Score=24.68 Aligned_cols=38 Identities=24% Similarity=0.405 Sum_probs=30.6
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCCcccccCCCCCCCCCCCCc
Q 029281 22 RPTDEELVVHYLKRKVFGLPLPASIIPELDVFQSHPLGLPGD 63 (196)
Q Consensus 22 ~PTDeELv~~YL~~k~~g~~l~~~~I~~~Dvy~~~Pw~Lp~~ 63 (196)
|-|..||++.-..--..|+|||.+ +|+...-|.++|..
T Consensus 51 hatnsellceaflhaftgqplptd----~dl~ker~deipe~ 88 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPTD----ADLRKERSDEIPEA 88 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCCc----HHHHHhccccchHH
Confidence 567888888777778899999864 58888888888865
No 7
>PF06404 PSK: Phytosulfokine precursor protein (PSK); InterPro: IPR009438 This family consists of several plant specific phytosulfokine precursor proteins. Phytosulfokines, are active as either a pentapeptide or a C-terminally truncated tetrapeptide. These compounds were first isolated because of their ability to stimulate cell division in somatic embryo cultures of Asparagus officinalis [].; GO: 0008083 growth factor activity, 0008283 cell proliferation, 0005576 extracellular region
Probab=32.33 E-value=16 Score=25.89 Aligned_cols=14 Identities=29% Similarity=0.873 Sum_probs=11.4
Q ss_pred CCCceeeeecccCC
Q 029281 182 FEPHISYIYSRDFD 195 (196)
Q Consensus 182 ~~~~~~~~~~~~~~ 195 (196)
-..|.+|||.|+-.
T Consensus 67 L~AHlDYIYTQ~~~ 80 (81)
T PF06404_consen 67 LAAHLDYIYTQHHN 80 (81)
T ss_pred HHHHhhheeccCCC
Confidence 35999999999853
No 8
>KOG1334 consensus WD40 repeat protein [General function prediction only]
Probab=29.53 E-value=77 Score=30.02 Aligned_cols=98 Identities=14% Similarity=0.244 Sum_probs=53.1
Q ss_pred HHHHHHHHHhhcCCC--------CCCCcccc------cCCCCCCCCCCCCcCCCCeEEEEecccccc----------cc-
Q 029281 27 ELVVHYLKRKVFGLP--------LPASIIPE------LDVFQSHPLGLPGDMKEKKRYFFSNIRNES----------AI- 81 (196)
Q Consensus 27 ELv~~YL~~k~~g~~--------l~~~~I~~------~Dvy~~~Pw~Lp~~~~~~~~yFFs~~~~~~----------~~- 81 (196)
|.+.-|=.|++...+ +|...+.+ .=+|.++|-+|.....+...|||++-+..- .+
T Consensus 304 qf~RvYD~R~~~~e~~n~~~~~f~p~hl~~d~~v~ITgl~Ysh~~sElLaSYnDe~IYLF~~~~~~G~~p~~~s~~~~~~ 383 (559)
T KOG1334|consen 304 QFARVYDQRRIDKEENNGVLDKFCPHHLVEDDPVNITGLVYSHDGSELLASYNDEDIYLFNKSMGDGSEPDPSSPREQYV 383 (559)
T ss_pred hhhhhhcccchhhccccchhhhcCCccccccCcccceeEEecCCccceeeeecccceEEeccccccCCCCCCCcchhhcc
Confidence 445557777776553 23333331 126778888888887788999996521111 00
Q ss_pred ---CCCCccccccC-CceeeecCCceeeEecCCCeE-EEEEEE---eeeecc
Q 029281 82 ---DNDGKCKIAAG-SGYWKPVGKNRQILASGTKQV-VGIRKT---LIFCEG 125 (196)
Q Consensus 82 ---~~g~R~~R~~g-~G~Wk~~g~~~~I~~~~~g~~-vG~kk~---l~F~~g 125 (196)
=.|.|-+|+++ --+|=... .-.|..+++|.| |+.|++ +.|.++
T Consensus 384 k~vYKGHrN~~TVKgVNFfGPrs-EyVvSGSDCGhIFiW~K~t~eii~~Meg 434 (559)
T KOG1334|consen 384 KRVYKGHRNSRTVKGVNFFGPRS-EYVVSGSDCGHIFIWDKKTGEIIRFMEG 434 (559)
T ss_pred chhhcccccccccceeeeccCcc-ceEEecCccceEEEEecchhHHHHHhhc
Confidence 02455566654 35663222 222223477776 666665 445554
No 9
>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=25.29 E-value=37 Score=26.30 Aligned_cols=11 Identities=55% Similarity=0.927 Sum_probs=9.4
Q ss_pred CCChHHHHHHH
Q 029281 22 RPTDEELVVHY 32 (196)
Q Consensus 22 ~PTDeELv~~Y 32 (196)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999865
No 10
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=25.11 E-value=38 Score=22.59 Aligned_cols=9 Identities=67% Similarity=0.981 Sum_probs=7.7
Q ss_pred CCChHHHHH
Q 029281 22 RPTDEELVV 30 (196)
Q Consensus 22 ~PTDeELv~ 30 (196)
+||||||..
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999864
Done!