Query 044940
Match_columns 226
No_of_seqs 161 out of 991
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 08:17:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044940hhsearch_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 6.1E-45 1.3E-49 287.7 6.9 127 8-141 1-129 (129)
2 PHA00692 hypothetical protein 41.0 11 0.00024 25.9 0.4 10 6-15 35-44 (74)
3 COG3060 MetJ Transcriptional r 29.1 44 0.00095 24.7 2.0 38 15-59 51-88 (105)
4 smart00265 BH4 BH4 Bcl-2 homol 28.8 56 0.0012 18.9 2.0 19 17-35 4-22 (27)
5 PF07960 CBP4: CBP4; InterPro 28.3 31 0.00067 27.4 1.2 11 15-25 30-40 (128)
6 cd00490 Met_repressor_MetJ Met 28.2 58 0.0013 24.2 2.5 38 15-59 50-87 (103)
7 smart00707 RPEL Repeat in Dros 27.1 44 0.00095 19.1 1.3 13 11-23 6-18 (26)
8 PRK05264 transcriptional repre 25.9 66 0.0014 24.1 2.4 38 15-59 51-88 (105)
9 PF08338 DUF1731: Domain of un 23.5 58 0.0013 21.1 1.6 17 10-26 31-48 (48)
10 PF13822 ACC_epsilon: Acyl-CoA 22.9 44 0.00095 22.9 1.0 9 15-23 10-18 (62)
11 PF01340 MetJ: Met Apo-repress 21.3 72 0.0016 23.8 1.9 38 15-59 50-87 (104)
12 PF06214 SLAM: Signaling lymph 20.0 24 0.00053 27.4 -0.8 30 46-77 94-123 (126)
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=6.1e-45 Score=287.69 Aligned_cols=127 Identities=39% Similarity=0.733 Sum_probs=92.6
Q ss_pred CCCCceeCCChHHHHHHHHhhhhcCCCCCCccceEEeccCCCCCCCCchhhhcCCCCCCCCceEEeeeccccccCCCCcc
Q 044940 8 LPVGCKFLPSDEQLVHYYLFNKISGIPTPFAEYFVKDVDLYDFDEPWDIWKRFGGTNLEDGEDIYFFTRLKKKSINGSRI 87 (226)
Q Consensus 8 LppGfRF~PTDeELi~~YL~~ki~g~~~p~~~~~I~~~Dvy~~~~Pw~L~~~~~~~~~~~~~~wyFFs~~~~~~~~g~R~ 87 (226)
|||||||+|||||||.+||++|+.|.+++. ..+|+++|||++ |||+|+..+. .++++||||+++++++.+|.|.
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~-~~~i~~~Diy~~-~P~~L~~~~~----~~~~~~yFF~~~~~~~~~~~r~ 74 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPC-EDVIHDVDIYSA-HPWELPAKFK----GGDEEWYFFSPRKKKYPNGGRP 74 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS--CHSEE--GGGS--GGGCHHHSS----S-SSEEEEEEE----------S
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCc-ccceeecccCcc-ChHHhhhhcc----CCCceEEEEEecccccCCcccc
Confidence 899999999999999999999999999887 367999999996 9999995432 2445799999999999999999
Q ss_pred cccccceeeeccCCCceEEeCCCCeeeeeEEEEeeecCCCC--CCcCeEEEEEEeC
Q 044940 88 DRKVGSGAWQGEAAGKLVRSCNFNRPIGSKKRFRYEKDNSP--HNGCWIMHEYTMN 141 (226)
Q Consensus 88 ~R~~~~G~Wk~~g~~k~I~~~~~g~~vG~kk~l~Fy~g~~~--~kT~WvMhEY~l~ 141 (226)
+|++++|+||++|+.+.|... +|.+||+|++|+||.++.+ .+|+|+||||+|.
T Consensus 75 ~R~~~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 75 NRVTGGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp -EEETTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cccccceEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999999999997 7999999999999976544 4899999999984
No 2
>PHA00692 hypothetical protein
Probab=40.99 E-value=11 Score=25.87 Aligned_cols=10 Identities=30% Similarity=0.408 Sum_probs=8.1
Q ss_pred CCCCCCceeC
Q 044940 6 RILPVGCKFL 15 (226)
Q Consensus 6 ~~LppGfRF~ 15 (226)
.+.||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4679999995
No 3
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=29.14 E-value=44 Score=24.70 Aligned_cols=38 Identities=21% Similarity=0.353 Sum_probs=30.1
Q ss_pred CCChHHHHHHHHhhhhcCCCCCCccceEEeccCCCCCCCCchhhh
Q 044940 15 LPSDEQLVHYYLFNKISGIPTPFAEYFVKDVDLYDFDEPWDIWKR 59 (226)
Q Consensus 15 ~PTDeELi~~YL~~ki~g~~~p~~~~~I~~~Dvy~~~~Pw~L~~~ 59 (226)
|-|..||++.-...-..|+|+|. |.|+.. .-|.++|+.
T Consensus 51 hatnsellceaflhaftgqplpt------d~dl~k-er~deipe~ 88 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT------DADLRK-ERSDEIPEA 88 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC------cHHHHH-hccccchHH
Confidence 56788888877777889999986 467875 478888875
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=28.85 E-value=56 Score=18.86 Aligned_cols=19 Identities=26% Similarity=0.252 Sum_probs=15.3
Q ss_pred ChHHHHHHHHhhhhcCCCC
Q 044940 17 SDEQLVHYYLFNKISGIPT 35 (226)
Q Consensus 17 TDeELi~~YL~~ki~g~~~ 35 (226)
+-.|||.+|+.-|+.-+-.
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4679999999999975543
No 5
>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=28.33 E-value=31 Score=27.36 Aligned_cols=11 Identities=36% Similarity=0.803 Sum_probs=9.2
Q ss_pred CCChHHHHHHH
Q 044940 15 LPSDEQLVHYY 25 (226)
Q Consensus 15 ~PTDeELi~~Y 25 (226)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999754
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=28.21 E-value=58 Score=24.21 Aligned_cols=38 Identities=21% Similarity=0.333 Sum_probs=29.7
Q ss_pred CCChHHHHHHHHhhhhcCCCCCCccceEEeccCCCCCCCCchhhh
Q 044940 15 LPSDEQLVHYYLFNKISGIPTPFAEYFVKDVDLYDFDEPWDIWKR 59 (226)
Q Consensus 15 ~PTDeELi~~YL~~ki~g~~~p~~~~~I~~~Dvy~~~~Pw~L~~~ 59 (226)
|-|.-||+|.-...-..|+|+|. |.|+-. +.|.++|+.
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~------D~Dl~K-~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD------DADLRK-ERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC------hhhhhh-cCcccccHH
Confidence 56788998887778889999997 347765 588888865
No 7
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=27.10 E-value=44 Score=19.11 Aligned_cols=13 Identities=23% Similarity=0.240 Sum_probs=11.0
Q ss_pred CceeCCChHHHHH
Q 044940 11 GCKFLPSDEQLVH 23 (226)
Q Consensus 11 GfRF~PTDeELi~ 23 (226)
...++|+-||||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
No 8
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=25.86 E-value=66 Score=24.07 Aligned_cols=38 Identities=18% Similarity=0.272 Sum_probs=29.6
Q ss_pred CCChHHHHHHHHhhhhcCCCCCCccceEEeccCCCCCCCCchhhh
Q 044940 15 LPSDEQLVHYYLFNKISGIPTPFAEYFVKDVDLYDFDEPWDIWKR 59 (226)
Q Consensus 15 ~PTDeELi~~YL~~ki~g~~~p~~~~~I~~~Dvy~~~~Pw~L~~~ 59 (226)
|-|.-||+|.-...-..|+|+|.+ -|+-. +.|.++|+.
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~D------~Dl~K-d~~d~ip~~ 88 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPDD------EDLRK-ERSDEIPEA 88 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCCh------hhhhh-cCcccchHH
Confidence 567889998877788899999973 47765 588888864
No 9
>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=23.53 E-value=58 Score=21.07 Aligned_cols=17 Identities=29% Similarity=0.491 Sum_probs=9.4
Q ss_pred CCceeC-CChHHHHHHHH
Q 044940 10 VGCKFL-PSDEQLVHYYL 26 (226)
Q Consensus 10 pGfRF~-PTDeELi~~YL 26 (226)
-||+|+ |+=++-+.+.|
T Consensus 31 ~GF~F~~p~l~~AL~~ll 48 (48)
T PF08338_consen 31 AGFQFRYPTLEEALRDLL 48 (48)
T ss_dssp TT---S-SSHHHHHHH--
T ss_pred CCCcccCCCHHHHHhccC
Confidence 599998 88888777643
No 10
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=22.94 E-value=44 Score=22.85 Aligned_cols=9 Identities=44% Similarity=0.719 Sum_probs=7.6
Q ss_pred CCChHHHHH
Q 044940 15 LPSDEQLVH 23 (226)
Q Consensus 15 ~PTDeELi~ 23 (226)
+||||||--
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999864
No 11
>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=21.32 E-value=72 Score=23.77 Aligned_cols=38 Identities=26% Similarity=0.402 Sum_probs=22.9
Q ss_pred CCChHHHHHHHHhhhhcCCCCCCccceEEeccCCCCCCCCchhhh
Q 044940 15 LPSDEQLVHYYLFNKISGIPTPFAEYFVKDVDLYDFDEPWDIWKR 59 (226)
Q Consensus 15 ~PTDeELi~~YL~~ki~g~~~p~~~~~I~~~Dvy~~~~Pw~L~~~ 59 (226)
|-|..||++.-...-..|+|+|. |.|+-. +.|..+|+.
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~------D~dl~k-d~~d~ip~~ 87 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT------DDDLRK-DRPDEIPAE 87 (104)
T ss_dssp S-SHHHHHHHHHHHHHH------------TTGGGS-TSGSSS-HH
T ss_pred hcccHHHHHHHHHHHhcCCCCCC------hhhhhh-cCCccchHH
Confidence 56888999887777889999997 347765 588888765
No 12
>PF06214 SLAM: Signaling lymphocytic activation molecule (SLAM) protein; InterPro: IPR010407 This entry is found in several mammalian signalling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70 kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones []. SLAM has also been recognised as a receptor for Measles virus [].; GO: 0004872 receptor activity, 0046649 lymphocyte activation, 0009986 cell surface, 0016021 integral to membrane; PDB: 3ALX_D 3ALZ_B 3ALW_A.
Probab=20.05 E-value=24 Score=27.41 Aligned_cols=30 Identities=23% Similarity=0.263 Sum_probs=15.2
Q ss_pred cCCCCCCCCchhhhcCCCCCCCCceEEeeecc
Q 044940 46 DLYDFDEPWDIWKRFGGTNLEDGEDIYFFTRL 77 (226)
Q Consensus 46 Dvy~~~~Pw~L~~~~~~~~~~~~~~wyFFs~~ 77 (226)
|=|.+ |+.+|--.--+... ..+.|||.+.-
T Consensus 94 dgY~F-hlEnLsL~Il~Srk-E~EGWYfmtlE 123 (126)
T PF06214_consen 94 DGYKF-HLENLSLEILESRK-EDEGWYFMTLE 123 (126)
T ss_dssp SSEEE-ETTTTEEEETT--G-GG-EEEEEEEE
T ss_pred cccEE-ecccceeehhcccc-ccCceEEEEee
Confidence 56666 67766433222222 23349998753
Done!