Query 047398
Match_columns 246
No_of_seqs 174 out of 974
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 10:43:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047398.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047398hhsearch_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 1.9E-44 4E-49 291.0 6.5 125 14-141 1-129 (129)
2 PHA03308 transcriptional regul 34.9 33 0.00071 35.9 2.8 16 186-201 1217-1232(1463)
3 PHA03308 transcriptional regul 30.4 55 0.0012 34.3 3.6 17 18-35 929-945 (1463)
4 PHA00692 hypothetical protein 29.0 22 0.00048 25.2 0.4 9 13-21 36-44 (74)
5 smart00265 BH4 BH4 Bcl-2 homol 27.9 73 0.0016 19.0 2.4 21 23-43 4-24 (27)
6 PF07960 CBP4: CBP4; InterPro 25.8 36 0.00079 27.7 1.2 11 21-31 30-40 (128)
7 cd00490 Met_repressor_MetJ Met 24.0 91 0.002 23.9 2.9 38 21-62 50-87 (103)
8 PF01340 MetJ: Met Apo-repress 22.1 92 0.002 24.0 2.6 38 21-62 50-87 (104)
9 PRK05264 transcriptional repre 21.5 99 0.0021 23.9 2.7 38 21-62 51-88 (105)
10 cd00950 DHDPS Dihydrodipicolin 20.9 78 0.0017 28.2 2.5 31 10-42 98-128 (284)
11 PF08338 DUF1731: Domain of un 20.3 73 0.0016 21.2 1.6 16 16-31 31-47 (48)
12 PLN02417 dihydrodipicolinate s 20.2 54 0.0012 29.6 1.3 22 10-32 99-120 (280)
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=1.9e-44 Score=290.98 Aligned_cols=125 Identities=52% Similarity=1.050 Sum_probs=94.6
Q ss_pred CCCCeeeCCCHHHHHHHHHHHHHcCCCCCC-CceecccCCCCCCCCCCC---ccccceeeeecccccCCCCCCccccccC
Q 047398 14 LPPGFRFQPTDDELVFQYLKCKVFSSPLPA-PIIPHINIYKYDPWDLPG---NLEQERYFFSNNEAKYPNGNRINRATAS 89 (246)
Q Consensus 14 LPpGfRF~PTDeELV~~YL~~K~~g~plp~-~~I~~vDVy~~~PwdLpg---~~~~e~YFFs~~~~k~~~g~R~~R~tg~ 89 (246)
|||||||+|||+|||.+||++|+.|.++|. .+|+++|||++|||+||+ ..+.+||||++++.++.+++|.+|++++
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 899999999999999999999999999998 799999999999999993 3347999999999999999999999999
Q ss_pred ceEeecccceeeeeCCCCceeeeeeEEEEEEeccCCCCCCCcCeEEEEEEeC
Q 047398 90 GYWKATGLDKQILSSSRINQMLMGMKKTLVFYRGKAPHESRTDWIMHEYRLV 141 (246)
Q Consensus 90 G~Wk~~G~~k~I~~~~~~~~~~vG~KktL~Fy~g~~~~g~rT~WvMhEY~L~ 141 (246)
|+||++|+.++|... ++.+ ||+|++|+||.++.+.+.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~--~g~~-iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDP--GGKV-IGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE---TTCE-EEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccc--ccee-eeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999985 4566 999999999998888889999999999984
No 2
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=34.87 E-value=33 Score=35.87 Aligned_cols=16 Identities=13% Similarity=0.355 Sum_probs=11.3
Q ss_pred CCCCCCeeeecccccc
Q 047398 186 PDQPQPRFYDFMMRDR 201 (246)
Q Consensus 186 ~~~~~~~~~df~~~~~ 201 (246)
...+..++|-+|++..
T Consensus 1217 igkasavlypymaqph 1232 (1463)
T PHA03308 1217 IGKASAVLYPYMAQPH 1232 (1463)
T ss_pred hcccceeechhccCcc
Confidence 3456778888888754
No 3
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=30.39 E-value=55 Score=34.26 Aligned_cols=17 Identities=29% Similarity=0.516 Sum_probs=10.7
Q ss_pred eeeCCCHHHHHHHHHHHH
Q 047398 18 FRFQPTDDELVFQYLKCK 35 (246)
Q Consensus 18 fRF~PTDeELV~~YL~~K 35 (246)
-+-+|+-+-|. .||+-.
T Consensus 929 ~~a~p~l~rla-~~l~~l 945 (1463)
T PHA03308 929 HRARPALERLA-NYLRGL 945 (1463)
T ss_pred hccchHHHHHH-HHHhcc
Confidence 45567777776 467653
No 4
>PHA00692 hypothetical protein
Probab=29.04 E-value=22 Score=25.18 Aligned_cols=9 Identities=67% Similarity=1.475 Sum_probs=7.8
Q ss_pred CCCCCeeeC
Q 047398 13 RLPPGFRFQ 21 (246)
Q Consensus 13 ~LPpGfRF~ 21 (246)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 589999995
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=27.95 E-value=73 Score=19.02 Aligned_cols=21 Identities=24% Similarity=0.330 Sum_probs=16.0
Q ss_pred CHHHHHHHHHHHHHcCCCCCC
Q 047398 23 TDDELVFQYLKCKVFSSPLPA 43 (246)
Q Consensus 23 TDeELV~~YL~~K~~g~plp~ 43 (246)
+-.|||+.|+.-|+.-...++
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCC
Confidence 567999999999987554443
No 6
>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=25.82 E-value=36 Score=27.74 Aligned_cols=11 Identities=45% Similarity=0.884 Sum_probs=9.4
Q ss_pred CCCHHHHHHHH
Q 047398 21 QPTDDELVFQY 31 (246)
Q Consensus 21 ~PTDeELV~~Y 31 (246)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999865
No 7
>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=24.04 E-value=91 Score=23.95 Aligned_cols=38 Identities=21% Similarity=0.357 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHHcCCCCCCCceecccCCCCCCCCCCCc
Q 047398 21 QPTDDELVFQYLKCKVFSSPLPAPIIPHINIYKYDPWDLPGN 62 (246)
Q Consensus 21 ~PTDeELV~~YL~~K~~g~plp~~~I~~vDVy~~~PwdLpg~ 62 (246)
|-|..||+..-...-..|+|||. +.|+-+..|-.+|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHH
Confidence 45677777665555778999997 568888899999865
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=22.07 E-value=92 Score=23.96 Aligned_cols=38 Identities=24% Similarity=0.423 Sum_probs=22.5
Q ss_pred CCCHHHHHHHHHHHHHcCCCCCCCceecccCCCCCCCCCCCc
Q 047398 21 QPTDDELVFQYLKCKVFSSPLPAPIIPHINIYKYDPWDLPGN 62 (246)
Q Consensus 21 ~PTDeELV~~YL~~K~~g~plp~~~I~~vDVy~~~PwdLpg~ 62 (246)
|-|..||+..-...-..|+|||. +.|+-+..|-.+|..
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~----D~dl~kd~~d~ip~~ 87 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT----DDDLRKDRPDEIPAE 87 (104)
T ss_dssp S-SHHHHHHHHHHHHHH----------TTGGGSTSGSSS-HH
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCCccchHH
Confidence 45777877665556778999996 568888999999865
No 9
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=21.50 E-value=99 Score=23.88 Aligned_cols=38 Identities=21% Similarity=0.341 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHHHcCCCCCCCceecccCCCCCCCCCCCc
Q 047398 21 QPTDDELVFQYLKCKVFSSPLPAPIIPHINIYKYDPWDLPGN 62 (246)
Q Consensus 21 ~PTDeELV~~YL~~K~~g~plp~~~I~~vDVy~~~PwdLpg~ 62 (246)
|-|..||+..-...-..|+|||. +.|+-+..|-++|..
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~ 88 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEA 88 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHH
Confidence 45677777665555778999997 568888899999864
No 10
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=20.91 E-value=78 Score=28.23 Aligned_cols=31 Identities=19% Similarity=0.323 Sum_probs=20.5
Q ss_pred CCcCCCCCeeeCCCHHHHHHHHHHHHHcCCCCC
Q 047398 10 GVTRLPPGFRFQPTDDELVFQYLKCKVFSSPLP 42 (246)
Q Consensus 10 ~~~~LPpGfRF~PTDeELV~~YL~~K~~g~plp 42 (246)
+.+-+||.| |.||+++|+. |.+.-+...++|
T Consensus 98 ~v~~~~P~~-~~~~~~~l~~-~~~~ia~~~~~p 128 (284)
T cd00950 98 AALVVTPYY-NKPSQEGLYA-HFKAIAEATDLP 128 (284)
T ss_pred EEEEccccc-CCCCHHHHHH-HHHHHHhcCCCC
Confidence 445677855 8899999995 555555544443
No 11
>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=20.29 E-value=73 Score=21.22 Aligned_cols=16 Identities=38% Similarity=0.721 Sum_probs=9.0
Q ss_pred CCeeeC-CCHHHHHHHH
Q 047398 16 PGFRFQ-PTDDELVFQY 31 (246)
Q Consensus 16 pGfRF~-PTDeELV~~Y 31 (246)
-||+|+ |+=++-+.+.
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 699998 8888776553
No 12
>PLN02417 dihydrodipicolinate synthase
Probab=20.22 E-value=54 Score=29.56 Aligned_cols=22 Identities=9% Similarity=0.315 Sum_probs=16.3
Q ss_pred CCcCCCCCeeeCCCHHHHHHHHH
Q 047398 10 GVTRLPPGFRFQPTDDELVFQYL 32 (246)
Q Consensus 10 ~~~~LPpGfRF~PTDeELV~~YL 32 (246)
+.+-+|| |-|.||+++|+.||-
T Consensus 99 av~~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 99 AALHINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EEEEcCC-ccCCCCHHHHHHHHH
Confidence 3456777 558999999997663
Done!