Query 045934
Match_columns 350
No_of_seqs 185 out of 951
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 07:01:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045934.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045934hhsearch_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 2.2E-44 4.7E-49 307.7 6.3 128 13-141 1-129 (129)
2 cd00933 barnase Barnase, a mem 26.4 1.9E+02 0.0041 24.7 5.6 61 22-96 2-70 (107)
3 PHA00692 hypothetical protein 24.3 28 0.00061 26.7 0.3 10 11-20 35-44 (74)
4 smart00265 BH4 BH4 Bcl-2 homol 17.4 1.5E+02 0.0032 19.3 2.4 19 22-40 4-22 (27)
5 PF07960 CBP4: CBP4; InterPro 17.0 69 0.0015 28.1 1.1 11 20-30 30-40 (128)
6 cd00490 Met_repressor_MetJ Met 16.8 1.2E+02 0.0025 25.2 2.3 39 20-62 50-88 (103)
7 PRK05264 transcriptional repre 15.1 1.3E+02 0.0027 25.2 2.1 39 20-62 51-89 (105)
8 COG3670 Lignostilbene-alpha,be 14.0 1E+02 0.0022 32.7 1.6 18 152-169 433-450 (490)
9 COG3060 MetJ Transcriptional r 13.1 1E+02 0.0023 25.3 1.1 39 20-62 51-89 (105)
10 PF01340 MetJ: Met Apo-repress 12.2 1.7E+02 0.0037 24.3 2.1 39 20-62 50-88 (104)
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=2.2e-44 Score=307.68 Aligned_cols=128 Identities=55% Similarity=1.169 Sum_probs=97.9
Q ss_pred CCCCceeCCChHHHHHHHHHHhHcCCCCCC-CceEeccCCCCCCCCcCccccCCCCeEEEeeccCCCCCCCCCCcccCCC
Q 045934 13 FPPGFRFHPSDQELIVYYLQNKVTSRPLPA-SLIAEVDLYKYNPWELPKQALFGEDEWFFFSPRDRKYPNGERPNRAAGS 91 (350)
Q Consensus 13 LPpGfRF~PTDEELV~~YL~~Ki~g~plp~-~vI~evDvy~~~PwdLP~~~~~g~~eWYFFs~r~rK~~~G~R~~Ratg~ 91 (350)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||+++||+||+....++++||||+++++++++|.|++|++++
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 899999999999999999999999999887 8999999999999999954444677999999999999999999999999
Q ss_pred CeEeeecCCccEEcCCCCeeEEEEEEEEEeeCCCCCCCCcCeEEEEEEeC
Q 045934 92 GYWKATGTDKPILSSVGSVNLGVKKALVFYTGRPPRGAKTDWMMNEYRLA 141 (350)
Q Consensus 92 G~WKatG~~k~I~~~~~g~vIG~KktL~Fy~gr~p~g~kT~WvMhEYrL~ 141 (350)
|+||++|++++|.+. +|.+||+|++|+||.++.+.+.+|+|+||||+|.
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 999999999999986 7899999999999998888899999999999984
No 2
>cd00933 barnase Barnase, a member of the family of homologous microbial ribonucleases, catalyses the cleavage of single-stranded RNA via a two-step mechanism thought to be similar to that of pancreatic ribonuclease. The mechanism involves a transesterification to give a 2', 3'-cyclic phosphate intermediate, followed by hydrolysis to yield a 3' nucleotide. The active site residues His and Glu act as general acid-base groups during catalysis, while the Arg and Lys residues are important in binding the reactive phosphate, the latter probably binding the phosphate in the transition state. Barstar, a small 89 residue intracellular protein is a natural inhibitor of Barnase.
Probab=26.36 E-value=1.9e+02 Score=24.68 Aligned_cols=61 Identities=26% Similarity=0.567 Sum_probs=33.7
Q ss_pred ChHHHHHHHHHHhHcCCCCCCCceEec--cCCCCC-----CCCc-CccccCCCCeEEEeeccCCCCCCCCCCcccCCCCe
Q 045934 22 SDQELIVYYLQNKVTSRPLPASLIAEV--DLYKYN-----PWEL-PKQALFGEDEWFFFSPRDRKYPNGERPNRAAGSGY 93 (350)
Q Consensus 22 TDEELV~~YL~~Ki~g~plp~~vI~ev--Dvy~~~-----PwdL-P~~~~~g~~eWYFFs~r~rK~~~G~R~~Ratg~G~ 93 (350)
|+.+-|..||.. .+ .||..+|.-. --.+.. .|+. |+++..|+- |.-+++..|. ..+|+
T Consensus 2 ~~~~~V~~y~~~--~~-~LP~~yiTK~ea~~lGW~~~~~~L~~~~pgk~igGd~----F~N~E~~LP~-------~~~~~ 67 (107)
T cd00933 2 NTFQGVADYLQT--YH-RLPDNYITKSQAKELGWVAPKGNLWDVAPGKSIGGDR----FSNREGRLPA-------AGGRT 67 (107)
T ss_pred chHHHHHHHHHH--hC-cCCcceEeHHHHHHhccCCCCCCHhHcCCCcccCCCe----EccCCCcCCC-------CCCCe
Confidence 455666789977 33 4898888643 223333 3332 555554442 5555544442 24678
Q ss_pred Eee
Q 045934 94 WKA 96 (350)
Q Consensus 94 WKa 96 (350)
|+-
T Consensus 68 y~E 70 (107)
T cd00933 68 WRE 70 (107)
T ss_pred EEE
Confidence 854
No 3
>PHA00692 hypothetical protein
Probab=24.35 E-value=28 Score=26.66 Aligned_cols=10 Identities=60% Similarity=1.530 Sum_probs=8.3
Q ss_pred CCCCCCceeC
Q 045934 11 FQFPPGFRFH 20 (350)
Q Consensus 11 ~~LPpGfRF~ 20 (350)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4679999995
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=17.38 E-value=1.5e+02 Score=19.27 Aligned_cols=19 Identities=26% Similarity=0.511 Sum_probs=15.0
Q ss_pred ChHHHHHHHHHHhHcCCCC
Q 045934 22 SDQELIVYYLQNKVTSRPL 40 (350)
Q Consensus 22 TDEELV~~YL~~Ki~g~pl 40 (350)
.-.|||++|+.-|+.-+-.
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999975543
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=17.02 E-value=69 Score=28.10 Aligned_cols=11 Identities=36% Similarity=0.791 Sum_probs=9.5
Q ss_pred CCChHHHHHHH
Q 045934 20 HPSDQELIVYY 30 (350)
Q Consensus 20 ~PTDEELV~~Y 30 (350)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
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=16.79 E-value=1.2e+02 Score=25.20 Aligned_cols=39 Identities=33% Similarity=0.543 Sum_probs=32.1
Q ss_pred CCChHHHHHHHHHHhHcCCCCCCCceEeccCCCCCCCCcCccc
Q 045934 20 HPSDQELIVYYLQNKVTSRPLPASLIAEVDLYKYNPWELPKQA 62 (350)
Q Consensus 20 ~PTDEELV~~YL~~Ki~g~plp~~vI~evDvy~~~PwdLP~~~ 62 (350)
|-|-.||++.-...-..|+|||. +.|+-+..|.++|+.+
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHHH
Confidence 56778888877778889999996 6699999999998754
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=15.08 E-value=1.3e+02 Score=25.16 Aligned_cols=39 Identities=33% Similarity=0.526 Sum_probs=32.0
Q ss_pred CCChHHHHHHHHHHhHcCCCCCCCceEeccCCCCCCCCcCccc
Q 045934 20 HPSDQELIVYYLQNKVTSRPLPASLIAEVDLYKYNPWELPKQA 62 (350)
Q Consensus 20 ~PTDEELV~~YL~~Ki~g~plp~~vI~evDvy~~~PwdLP~~~ 62 (350)
|-|-.||++.-...-..|+|||. +.|+.+..|.++|+.+
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 56778888877778889999996 5699999999998654
No 8
>COG3670 Lignostilbene-alpha,beta-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=14.00 E-value=1e+02 Score=32.71 Aligned_cols=18 Identities=28% Similarity=0.410 Sum_probs=13.8
Q ss_pred CCCcCCceEEEEEEecCC
Q 045934 152 GSMRLDDWVLCRVRHKSN 169 (350)
Q Consensus 152 ~~~~~~e~VLCRIy~k~~ 169 (350)
+..+.+.|+||-||.-.+
T Consensus 433 ~~~EdDGwLl~~vyd~~~ 450 (490)
T COG3670 433 SSAEDDGWLLTLVYDGDR 450 (490)
T ss_pred CCcCCCcEEEEEEEecCC
Confidence 445678899999997654
No 9
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=13.12 E-value=1e+02 Score=25.33 Aligned_cols=39 Identities=33% Similarity=0.550 Sum_probs=31.7
Q ss_pred CCChHHHHHHHHHHhHcCCCCCCCceEeccCCCCCCCCcCccc
Q 045934 20 HPSDQELIVYYLQNKVTSRPLPASLIAEVDLYKYNPWELPKQA 62 (350)
Q Consensus 20 ~PTDEELV~~YL~~Ki~g~plp~~vI~evDvy~~~PwdLP~~~ 62 (350)
|-|..||++.-...-..|+|||. +.|+.+.-|.++|+.+
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHH
Confidence 56777888777778889999985 6789998999998765
No 10
>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=12.19 E-value=1.7e+02 Score=24.31 Aligned_cols=39 Identities=36% Similarity=0.588 Sum_probs=25.3
Q ss_pred CCChHHHHHHHHHHhHcCCCCCCCceEeccCCCCCCCCcCccc
Q 045934 20 HPSDQELIVYYLQNKVTSRPLPASLIAEVDLYKYNPWELPKQA 62 (350)
Q Consensus 20 ~PTDEELV~~YL~~Ki~g~plp~~vI~evDvy~~~PwdLP~~~ 62 (350)
|-|-.||++.-...-..|+|||. +.|+-+..|.++|...
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 56788888877778889999995 5699999999998754
Done!