Query 017854
Match_columns 365
No_of_seqs 194 out of 974
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:00:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017854.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017854hhsearch_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 5.3E-43 1.1E-47 299.9 4.7 128 15-143 1-129 (129)
2 PF07051 OCIA: Ovarian carcino 27.5 61 0.0013 28.2 2.9 30 1-30 1-33 (111)
3 smart00265 BH4 BH4 Bcl-2 homol 16.1 1.2E+02 0.0026 20.1 1.8 18 23-40 3-20 (27)
4 PHA00692 hypothetical protein 16.1 59 0.0013 25.5 0.4 10 13-22 35-44 (74)
5 cd00490 Met_repressor_MetJ Met 14.3 1.7E+02 0.0036 24.8 2.7 39 22-64 50-88 (103)
6 PRK05264 transcriptional repre 12.7 1.8E+02 0.0039 24.8 2.4 39 22-64 51-89 (105)
7 PF07960 CBP4: CBP4; InterPro 12.5 1.1E+02 0.0023 27.3 1.1 11 22-32 30-40 (128)
8 COG3060 MetJ Transcriptional r 12.5 1.1E+02 0.0024 25.7 1.1 39 22-64 51-89 (105)
9 PF01340 MetJ: Met Apo-repress 11.1 2E+02 0.0042 24.4 2.2 39 22-64 50-88 (104)
10 PF04700 Baculo_gp41: Structur 10.9 2.2E+02 0.0049 26.9 2.7 24 20-44 3-28 (186)
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=5.3e-43 Score=299.86 Aligned_cols=128 Identities=59% Similarity=1.206 Sum_probs=96.8
Q ss_pred CCCCceeCCChHHHHHHHHHHhHcCCCCCc-ceeeecCCCCCCCCCCCccccCCCceEEEeccCCCCCCCCCCCccccCC
Q 017854 15 LPPGFRFHPTDEELVVHYLKKKAASAPLPV-AIIAEVDLYKFDPWELPSKATFGEQEWYFFSPRDRKYPNGARPNRAATS 93 (365)
Q Consensus 15 LPpGfRF~PTDEELV~~YL~~Ki~G~plp~-~iI~evDVY~~ePwdLP~~~~~ge~eWYFFspr~rK~~nG~R~~R~tgg 93 (365)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+||+....++++||||+++++++.++.|.+|++++
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 7899999999999999954444677999999999999999999999999
Q ss_pred CeeeecCCCceeecCCCceeeeeeEEEEEecCCCCCCCCcCeEEEEEEec
Q 017854 94 GYWKATGTDKPILTSKGNQKVGVKKALVFYGGKPPKGIKTNWIMHEYRIV 143 (365)
Q Consensus 94 G~WKatG~~k~I~~~~G~~~VG~KKtLvFy~gk~p~g~KT~WvMhEY~L~ 143 (365)
|+||.+|++++|.+. ++++||+|++|+||.++.+++.+|+|+||||+|.
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 999999999999876 5689999999999998888899999999999984
No 2
>PF07051 OCIA: Ovarian carcinoma immunoreactive antigen (OCIA); InterPro: IPR009764 This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown [,].
Probab=27.53 E-value=61 Score=28.20 Aligned_cols=30 Identities=33% Similarity=0.382 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCCCC---CCCCceeCCChHHHHH
Q 017854 1 MESTDSSTSSQHPQ---LPPGFRFHPTDEELVV 30 (365)
Q Consensus 1 m~~~~~s~~~~~~~---LPpGfRF~PTDEELV~ 30 (365)
|+++.++...++.. -+++-.+.+||||+-+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~T~EE~kv 33 (111)
T PF07051_consen 1 MMSRFSDQQQQQHHPPPPHPGMPYQLTEEERKV 33 (111)
T ss_pred CccccccccCCCCCCCCCCCCcCccCCHHHHHH
Confidence 77777666544332 3679999999999754
No 3
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=16.13 E-value=1.2e+02 Score=20.13 Aligned_cols=18 Identities=33% Similarity=0.477 Sum_probs=14.2
Q ss_pred CChHHHHHHHHHHhHcCC
Q 017854 23 PTDEELVVHYLKKKAASA 40 (365)
Q Consensus 23 PTDEELV~~YL~~Ki~G~ 40 (365)
.+-.|||.+|+.-|+.-.
T Consensus 3 ~~nRelV~~yv~yKLsQr 20 (27)
T smart00265 3 LDNRELVVDYVTYKLSQN 20 (27)
T ss_pred cchHHHHHHHHHHHHhhc
Confidence 356899999999998643
No 4
>PHA00692 hypothetical protein
Probab=16.05 E-value=59 Score=25.51 Aligned_cols=10 Identities=60% Similarity=1.298 Sum_probs=7.7
Q ss_pred CCCCCCceeC
Q 017854 13 PQLPPGFRFH 22 (365)
Q Consensus 13 ~~LPpGfRF~ 22 (365)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4579999994
No 5
>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=14.30 E-value=1.7e+02 Score=24.83 Aligned_cols=39 Identities=33% Similarity=0.435 Sum_probs=31.8
Q ss_pred CCChHHHHHHHHHHhHcCCCCCcceeeecCCCCCCCCCCCccc
Q 017854 22 HPTDEELVVHYLKKKAASAPLPVAIIAEVDLYKFDPWELPSKA 64 (365)
Q Consensus 22 ~PTDEELV~~YL~~Ki~G~plp~~iI~evDVY~~ePwdLP~~~ 64 (365)
|-|.-||++.-...-..|+|||.+ .|+-+..|.++|+..
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 567788888777778899999974 688888999998754
No 6
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=12.66 E-value=1.8e+02 Score=24.76 Aligned_cols=39 Identities=33% Similarity=0.418 Sum_probs=31.6
Q ss_pred CCChHHHHHHHHHHhHcCCCCCcceeeecCCCCCCCCCCCccc
Q 017854 22 HPTDEELVVHYLKKKAASAPLPVAIIAEVDLYKFDPWELPSKA 64 (365)
Q Consensus 22 ~PTDEELV~~YL~~Ki~G~plp~~iI~evDVY~~ePwdLP~~~ 64 (365)
|-|.-||++.-...-..|+|||.+ .|+-+..|.++|+.+
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~D----~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPDD----EDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCCh----hhhhhcCcccchHHH
Confidence 567788888777778899999974 688888999998653
No 7
>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=12.51 E-value=1.1e+02 Score=27.33 Aligned_cols=11 Identities=55% Similarity=0.924 Sum_probs=9.8
Q ss_pred CCChHHHHHHH
Q 017854 22 HPTDEELVVHY 32 (365)
Q Consensus 22 ~PTDEELV~~Y 32 (365)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 79999999876
No 8
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=12.50 E-value=1.1e+02 Score=25.73 Aligned_cols=39 Identities=33% Similarity=0.486 Sum_probs=31.5
Q ss_pred CCChHHHHHHHHHHhHcCCCCCcceeeecCCCCCCCCCCCccc
Q 017854 22 HPTDEELVVHYLKKKAASAPLPVAIIAEVDLYKFDPWELPSKA 64 (365)
Q Consensus 22 ~PTDEELV~~YL~~Ki~G~plp~~iI~evDVY~~ePwdLP~~~ 64 (365)
|-|..||++.-...-..|+|||. +.|+.+.-|.++|+.+
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHH
Confidence 56778888877777889999996 3688888899998754
No 9
>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=11.10 E-value=2e+02 Score=24.45 Aligned_cols=39 Identities=36% Similarity=0.512 Sum_probs=24.7
Q ss_pred CCChHHHHHHHHHHhHcCCCCCcceeeecCCCCCCCCCCCccc
Q 017854 22 HPTDEELVVHYLKKKAASAPLPVAIIAEVDLYKFDPWELPSKA 64 (365)
Q Consensus 22 ~PTDEELV~~YL~~Ki~G~plp~~iI~evDVY~~ePwdLP~~~ 64 (365)
|-|.-||++.-...-..|+|||.+ .|+-+..|.++|...
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~D----~dl~kd~~d~ip~~~ 88 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPTD----DDLRKDRPDEIPAEA 88 (104)
T ss_dssp S-SHHHHHHHHHHHHHH------T----TGGGSTSGSSS-HHH
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcCCccchHHH
Confidence 567888888777778899999974 688889999998753
No 10
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=10.93 E-value=2.2e+02 Score=26.86 Aligned_cols=24 Identities=42% Similarity=0.685 Sum_probs=15.6
Q ss_pred eeCCChHHHHHHHH--HHhHcCCCCCc
Q 017854 20 RFHPTDEELVVHYL--KKKAASAPLPV 44 (365)
Q Consensus 20 RF~PTDEELV~~YL--~~Ki~G~plp~ 44 (365)
|| =+|||||.||- .+|..|...+.
T Consensus 3 RF-~sDe~Li~yY~~L~K~~g~~~~~~ 28 (186)
T PF04700_consen 3 RF-ESDEELIEYYANLEKKYGGSDVPS 28 (186)
T ss_pred cc-ccHHHHHHHHHHHHHHhCCCCCCc
Confidence 45 48999999885 45555554443
Done!