Query 021910
Match_columns 305
No_of_seqs 183 out of 994
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 06:35:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021910.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021910hhsearch_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 3.9E-43 8.5E-48 293.7 5.5 126 9-134 1-129 (129)
2 PHA00692 hypothetical protein 17.9 45 0.00098 25.3 0.2 10 7-16 35-44 (74)
3 PF07960 CBP4: CBP4; InterPro 15.9 77 0.0017 27.4 1.2 11 16-26 30-40 (128)
4 smart00265 BH4 BH4 Bcl-2 homol 12.2 2.2E+02 0.0047 18.3 2.1 19 18-36 4-22 (27)
5 smart00707 RPEL Repeat in Dros 11.9 1.5E+02 0.0032 18.8 1.3 13 12-24 6-18 (26)
6 cd00490 Met_repressor_MetJ Met 11.7 2.3E+02 0.0051 23.2 2.7 39 16-58 50-88 (103)
7 PRK05264 transcriptional repre 11.2 2.1E+02 0.0046 23.6 2.4 38 16-57 51-88 (105)
8 PF08338 DUF1731: Domain of un 11.1 1.7E+02 0.0037 20.7 1.6 16 11-26 31-47 (48)
9 PF13822 ACC_epsilon: Acyl-CoA 11.0 1.3E+02 0.0028 22.4 1.0 9 16-24 10-18 (62)
10 COG3100 Uncharacterized protei 10.9 1.6E+02 0.0036 24.3 1.6 16 151-166 10-25 (103)
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=3.9e-43 Score=293.74 Aligned_cols=126 Identities=60% Similarity=1.206 Sum_probs=95.9
Q ss_pred CCCceeeCCChHHHHHHHHHHhhcCCCCCC-CceeeccCCCCCCCCCccccccCCeeEEEecccCCCCCCCCCCceecCC
Q 021910 9 LPPGFRFHPTDEELVNHYLCRKCAGLPISV-PIIAEIDLYKYDPWELPEMARYGEKEWYFFSPRDRKYPNGSRPNRAAGS 87 (305)
Q Consensus 9 LPpGfRF~PTDeELV~~YL~~Ki~G~pl~~-~iI~evDVY~~ePwdLP~~~~~ge~eWYFFspr~rk~~~G~R~~RaaGg 87 (305)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+||+....++++||||+++++++.+|+|.+|++++
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 899999999999999999999999999888 7999999999999999954444677999999999999999999999999
Q ss_pred CeEEecccccccC--CCcceeEEEEEEeecCCCCCCCccCeEEEEEeeC
Q 021910 88 GYWKATGADKPIG--KPKTLGIKKALVFYAGKAPKGIKTNWIMHEYRPA 134 (305)
Q Consensus 88 G~WK~tG~~k~V~--~gk~vG~KktL~Fy~gk~p~g~KT~WiMhEY~L~ 134 (305)
|+||.+|+.++|. ++++||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999985 5899999999999998888899999999999983
No 2
>PHA00692 hypothetical protein
Probab=17.94 E-value=45 Score=25.30 Aligned_cols=10 Identities=70% Similarity=1.481 Sum_probs=7.8
Q ss_pred CCCCCceeeC
Q 021910 7 LELPPGFRFH 16 (305)
Q Consensus 7 ~~LPpGfRF~ 16 (305)
+..||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 3579999985
No 3
>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=15.92 E-value=77 Score=27.37 Aligned_cols=11 Identities=55% Similarity=0.999 Sum_probs=9.5
Q ss_pred CCChHHHHHHH
Q 021910 16 HPTDEELVNHY 26 (305)
Q Consensus 16 ~PTDeELV~~Y 26 (305)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 59999999875
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=12.25 E-value=2.2e+02 Score=18.27 Aligned_cols=19 Identities=26% Similarity=0.275 Sum_probs=14.9
Q ss_pred ChHHHHHHHHHHhhcCCCC
Q 021910 18 TDEELVNHYLCRKCAGLPI 36 (305)
Q Consensus 18 TDeELV~~YL~~Ki~G~pl 36 (305)
+-.|||.+|+.-|+.-...
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999965443
No 5
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=11.88 E-value=1.5e+02 Score=18.80 Aligned_cols=13 Identities=38% Similarity=0.480 Sum_probs=10.7
Q ss_pred ceeeCCChHHHHH
Q 021910 12 GFRFHPTDEELVN 24 (305)
Q Consensus 12 GfRF~PTDeELV~ 24 (305)
....+||.+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3467899999997
No 6
>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=11.67 E-value=2.3e+02 Score=23.19 Aligned_cols=39 Identities=33% Similarity=0.433 Sum_probs=31.3
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCCceeeccCCCCCCCCCcccc
Q 021910 16 HPTDEELVNHYLCRKCAGLPISVPIIAEIDLYKYDPWELPEMA 58 (305)
Q Consensus 16 ~PTDeELV~~YL~~Ki~G~pl~~~iI~evDVY~~ePwdLP~~~ 58 (305)
|-|-.||+.--...-..|+|||.+ .|+-+..|.++|+.+
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 567788887777788899999865 588889999999753
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=11.20 E-value=2.1e+02 Score=23.56 Aligned_cols=38 Identities=32% Similarity=0.406 Sum_probs=30.8
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCCceeeccCCCCCCCCCccc
Q 021910 16 HPTDEELVNHYLCRKCAGLPISVPIIAEIDLYKYDPWELPEM 57 (305)
Q Consensus 16 ~PTDeELV~~YL~~Ki~G~pl~~~iI~evDVY~~ePwdLP~~ 57 (305)
|-|-.||+.--...-..|+|||.+ .|+-+..|.++|+.
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 567788887777788899999865 58888999999965
No 8
>PF08338 DUF1731: Domain of unknown function (DUF1731); InterPro: IPR013549 This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (IPR001509 from INTERPRO) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. ; PDB: 3OH8_A.
Probab=11.09 E-value=1.7e+02 Score=20.70 Aligned_cols=16 Identities=44% Similarity=0.783 Sum_probs=9.2
Q ss_pred CceeeC-CChHHHHHHH
Q 021910 11 PGFRFH-PTDEELVNHY 26 (305)
Q Consensus 11 pGfRF~-PTDeELV~~Y 26 (305)
.||+|+ |+=++.+.+.
T Consensus 31 ~GF~F~~p~l~~AL~~l 47 (48)
T PF08338_consen 31 AGFQFRYPTLEEALRDL 47 (48)
T ss_dssp TT---S-SSHHHHHHH-
T ss_pred CCCcccCCCHHHHHhcc
Confidence 599998 8888777654
No 9
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=10.98 E-value=1.3e+02 Score=22.40 Aligned_cols=9 Identities=67% Similarity=0.999 Sum_probs=7.4
Q ss_pred CCChHHHHH
Q 021910 16 HPTDEELVN 24 (305)
Q Consensus 16 ~PTDeELV~ 24 (305)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 699999865
No 10
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=10.87 E-value=1.6e+02 Score=24.32 Aligned_cols=16 Identities=19% Similarity=0.413 Sum_probs=12.4
Q ss_pred EEEEEEEeeCCCCCCC
Q 021910 151 WVLCRLYNKKGRMEKH 166 (305)
Q Consensus 151 ~VLCRIy~Kk~~~ek~ 166 (305)
-.||-||+++++..-.
T Consensus 10 ~mlCaIYkS~kk~~tY 25 (103)
T COG3100 10 SMLCAIYKSPKKDGTY 25 (103)
T ss_pred eeeeeeeecCcCCccE
Confidence 4799999988776554
Done!