Query 037591
Match_columns 331
No_of_seqs 184 out of 977
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 02:30:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037591.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037591hhsearch_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 6.2E-44 1.3E-48 302.0 6.1 128 10-138 1-129 (129)
2 KOG4286 Dystrophin-like protei 37.0 8.4 0.00018 42.5 -1.0 55 107-161 613-678 (966)
3 cd00490 Met_repressor_MetJ Met 19.4 73 0.0016 26.4 1.7 40 17-60 50-89 (103)
4 smart00265 BH4 BH4 Bcl-2 homol 17.7 1.3E+02 0.0027 19.6 2.2 20 19-38 4-23 (27)
5 PHA00692 hypothetical protein 17.1 52 0.0011 25.3 0.4 10 8-17 35-44 (74)
6 PRK05264 transcriptional repre 16.6 85 0.0018 26.2 1.5 39 17-59 51-89 (105)
7 COG3060 MetJ Transcriptional r 14.9 71 0.0015 26.3 0.7 40 17-60 51-90 (105)
8 PF01340 MetJ: Met Apo-repress 13.3 1E+02 0.0022 25.6 1.2 39 17-59 50-88 (104)
9 PF07960 CBP4: CBP4; InterPro 13.0 1E+02 0.0022 27.0 1.2 14 14-27 26-40 (128)
10 PRK15244 virulence protein Spv 12.0 1.1E+02 0.0025 33.0 1.3 20 257-277 358-377 (591)
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=6.2e-44 Score=301.98 Aligned_cols=128 Identities=55% Similarity=1.070 Sum_probs=97.5
Q ss_pred CCCcceECCCHHHHHHHHHHHhhcCCCCCc-cceeccCCCCCCCCCCCCcccCCCeeEEEEeecCCcCCCCCccccccCC
Q 037591 10 LPPGFRFHPSDEELITYYLVNKISDASFTG-RAIADVDLNKCEPWDLPGKAKMGEKEWYFFSLRDRKYPTGVRTNRATNT 88 (331)
Q Consensus 10 LPpGfRF~PTDEELI~~YL~~Ki~g~p~~~-~~I~dvDly~~ePWdLP~~~~~ge~eWYFFs~r~rk~~~G~R~nRat~~ 88 (331)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+||.....++++||||+++++++.+|.|.+|++++
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 899999999999999999999999998766 7899999999999999954445678999999999999999999999999
Q ss_pred CceeecCCCeeEEeCCCCeEEeEEEEEEEeecCCCCCCccCeEEEEEEeC
Q 037591 89 GYWKTTGKDKEIFNSVTSELVGMKKTLVFYRGRAPRGEKTNWVMHEYRIH 138 (331)
Q Consensus 89 GyWKatGk~k~I~~~~~g~vIG~KKtLvFY~gr~pkg~KT~WvMhEY~L~ 138 (331)
|+||.+|+.+.|.+. ++.+||+||+|+||.++.+++.||+|+||||+|.
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 999999999999975 7899999999999999889999999999999984
No 2
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=36.99 E-value=8.4 Score=42.45 Aligned_cols=55 Identities=25% Similarity=0.436 Sum_probs=38.7
Q ss_pred eEEeEE-EEEE----------EeecCCCCCCccCeEEEEEEeCCCCCcCCCCCcEEEEEEEEcCCC
Q 037591 107 ELVGMK-KTLV----------FYRGRAPRGEKTNWVMHEYRIHSKSAFRTSKDEWVVCRVFQKSAG 161 (331)
Q Consensus 107 ~vIG~K-KtLv----------FY~gr~pkg~KT~WvMhEY~L~~~~~~~~~~~e~VLCRVf~K~~~ 161 (331)
-|||+| |+++ |..||+.++.|++.-|.||.....++.+...---|||--|+.++.
T Consensus 613 pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tts~~d~rdfak~L~nkfr~~~~ 678 (966)
T KOG4286|consen 613 PIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKRY 678 (966)
T ss_pred ccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCCChhhHHHHHHHHHhhhccchh
Confidence 588988 5554 677999999999999999999876542211122377777765543
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=19.36 E-value=73 Score=26.41 Aligned_cols=40 Identities=25% Similarity=0.434 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCccceeccCCCCCCCCCCCCccc
Q 037591 17 HPSDEELITYYLVNKISDASFTGRAIADVDLNKCEPWDLPGKAK 60 (331)
Q Consensus 17 ~PTDEELI~~YL~~Ki~g~p~~~~~I~dvDly~~ePWdLP~~~~ 60 (331)
|-|.-||+|.-...-..|+|+|. |-||-+..|.++|..++
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ak 89 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEAAK 89 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHHHH
Confidence 56788999886667888999886 67899999999998653
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=17.66 E-value=1.3e+02 Score=19.63 Aligned_cols=20 Identities=25% Similarity=0.557 Sum_probs=15.9
Q ss_pred CHHHHHHHHHHHhhcCCCCC
Q 037591 19 SDEELITYYLVNKISDASFT 38 (331)
Q Consensus 19 TDEELI~~YL~~Ki~g~p~~ 38 (331)
.-.|||.+|+.-|+.-...+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999876443
No 5
>PHA00692 hypothetical protein
Probab=17.09 E-value=52 Score=25.32 Aligned_cols=10 Identities=60% Similarity=1.235 Sum_probs=8.0
Q ss_pred CCCCCcceEC
Q 037591 8 ETLPPGFRFH 17 (331)
Q Consensus 8 ~~LPpGfRF~ 17 (331)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4579999995
No 6
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=16.56 E-value=85 Score=26.18 Aligned_cols=39 Identities=23% Similarity=0.400 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCccceeccCCCCCCCCCCCCcc
Q 037591 17 HPSDEELITYYLVNKISDASFTGRAIADVDLNKCEPWDLPGKA 59 (331)
Q Consensus 17 ~PTDEELI~~YL~~Ki~g~p~~~~~I~dvDly~~ePWdLP~~~ 59 (331)
|-|.-||+|.-...-..|+|+|. |-||-+..|.++|..+
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHHH
Confidence 56788999886667888999885 6789999999999764
No 7
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=14.86 E-value=71 Score=26.32 Aligned_cols=40 Identities=25% Similarity=0.424 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCccceeccCCCCCCCCCCCCccc
Q 037591 17 HPSDEELITYYLVNKISDASFTGRAIADVDLNKCEPWDLPGKAK 60 (331)
Q Consensus 17 ~PTDEELI~~YL~~Ki~g~p~~~~~I~dvDly~~ePWdLP~~~~ 60 (331)
|-|.-||+|.-...-..|+|+|. |.||-+.-|.++|+.++
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~ak 90 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAAK 90 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHHH
Confidence 56778888886667888998874 77899999999998754
No 8
>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=13.27 E-value=1e+02 Score=25.59 Aligned_cols=39 Identities=26% Similarity=0.466 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCccceeccCCCCCCCCCCCCcc
Q 037591 17 HPSDEELITYYLVNKISDASFTGRAIADVDLNKCEPWDLPGKA 59 (331)
Q Consensus 17 ~PTDEELI~~YL~~Ki~g~p~~~~~I~dvDly~~ePWdLP~~~ 59 (331)
|-|.-||+|.-...-..|+|+|. |.||-+..|-++|..+
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~----D~dl~kd~~d~ip~~~ 88 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT----DDDLRKDRPDEIPAEA 88 (104)
T ss_dssp S-SHHHHHHHHHHHHHH----------TTGGGSTSGSSS-HHH
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCCccchHHH
Confidence 56888999886667888999875 6789999999999764
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=13.00 E-value=1e+02 Score=26.96 Aligned_cols=14 Identities=36% Similarity=0.897 Sum_probs=10.7
Q ss_pred ceE-CCCHHHHHHHH
Q 037591 14 FRF-HPSDEELITYY 27 (331)
Q Consensus 14 fRF-~PTDEELI~~Y 27 (331)
|++ .||||||+..|
T Consensus 26 ~~y~tPTeEeL~~r~ 40 (128)
T PF07960_consen 26 VKYTTPTEEELFKRY 40 (128)
T ss_pred heecCCCHHHHHHhc
Confidence 344 59999999874
No 10
>PRK15244 virulence protein SpvB; Provisional
Probab=11.97 E-value=1.1e+02 Score=32.96 Aligned_cols=20 Identities=40% Similarity=0.800 Sum_probs=11.8
Q ss_pred cCCCccCCCCCCCCCccccch
Q 037591 257 TTQPVLRPMPPPPPHPQAMHQ 277 (331)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~~~~ 277 (331)
.-.| ..+||||||+|++|.-
T Consensus 358 ~~~~-~~~~~~~~~~~~~~~~ 377 (591)
T PRK15244 358 RRAP-VNNMMPPPPPPPMMGG 377 (591)
T ss_pred cccc-CCCCCCCcccCcccCC
Confidence 4456 5667666666655544
Done!