Query 047710
Match_columns 384
No_of_seqs 224 out of 984
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 13:53:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047710.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047710hhsearch_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 1.8E-43 3.9E-48 304.6 6.7 128 15-143 1-129 (129)
2 PHA00692 hypothetical protein 20.9 36 0.00077 26.9 0.2 10 13-22 35-44 (74)
3 cd00490 Met_repressor_MetJ Met 19.3 86 0.0019 26.7 2.2 40 22-65 50-89 (103)
4 COG3060 MetJ Transcriptional r 17.9 66 0.0014 27.2 1.2 40 22-65 51-90 (105)
5 smart00265 BH4 BH4 Bcl-2 homol 17.6 1.3E+02 0.0029 20.1 2.3 21 24-44 4-24 (27)
6 PF15355 Chisel: Stretch-respo 17.3 44 0.00095 27.7 0.0 15 315-329 7-21 (87)
7 PRK05264 transcriptional repre 16.7 99 0.0021 26.5 1.9 40 22-65 51-90 (105)
8 KOG1214 Nidogen and related ba 15.8 66 0.0014 37.2 0.9 38 294-331 1159-1204(1289)
9 PF11535 Calci_bind_CcbP: Calc 14.3 56 0.0012 28.2 -0.1 10 320-329 25-34 (106)
10 PF01340 MetJ: Met Apo-repress 13.0 1.3E+02 0.0027 25.8 1.6 39 22-64 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=1.8e-43 Score=304.59 Aligned_cols=128 Identities=57% Similarity=1.071 Sum_probs=97.9
Q ss_pred CCCCeeECCChHHHHHHHHHhhhcCCCCCC-CceeeccCCCCCCCCCCccccCCCeeEEEeccCCccCCCCCCcccccCC
Q 047710 15 LPPGFRFHPTDEELITYYLLKKVLDCNFTG-RAIAEVDLNKCEPWELPAKAKMGEKEWYFFSLRDRKYPTGLRTNRATEA 93 (384)
Q Consensus 15 LPPGFRF~PTDEELI~~YL~~Kv~g~pl~~-~~I~evDVY~~ePWdLP~~~~~gekeWYFFs~r~rKy~~G~R~nRat~g 93 (384)
|||||||+|||||||.+||++|+.+.+++. .+|+++|||.+|||+||.....++++||||+++++++.+|.|.+|++++
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 899999999999999999999999998877 7899999999999999965555678999999999999999999999999
Q ss_pred ceEeecCCceeeeeCCCceeeeeEEEEEeeecCCCCCCccCeEEEEEEeC
Q 047710 94 GYWKATGKDREIYSSKTCALVGMKKTLVFYRGRAPKGEKSNWVMHEYRLE 143 (384)
Q Consensus 94 GyWKatGkdk~I~~~~~G~vVG~KKtLvFY~Grapkg~KT~WvMhEYrL~ 143 (384)
|+||.+|+++.|.+. ++.+||+||+|+||.++.+++.||+|+||||+|+
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 999999999999985 6899999999999999889999999999999985
No 2
>PHA00692 hypothetical protein
Probab=20.94 E-value=36 Score=26.95 Aligned_cols=10 Identities=60% Similarity=1.318 Sum_probs=8.4
Q ss_pred CCCCCCeeEC
Q 047710 13 AHLPPGFRFH 22 (384)
Q Consensus 13 ~~LPPGFRF~ 22 (384)
.+.||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4789999995
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=19.32 E-value=86 Score=26.72 Aligned_cols=40 Identities=30% Similarity=0.393 Sum_probs=33.5
Q ss_pred CCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCCCCcccc
Q 047710 22 HPTDEELITYYLLKKVLDCNFTGRAIAEVDLNKCEPWELPAKAK 65 (384)
Q Consensus 22 ~PTDEELI~~YL~~Kv~g~pl~~~~I~evDVY~~ePWdLP~~~~ 65 (384)
|-|..||++.-.+.-..|.|+|. +.||-+..|.++|+.++
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 56788999887778888999887 67899999999997753
No 4
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=17.91 E-value=66 Score=27.22 Aligned_cols=40 Identities=30% Similarity=0.383 Sum_probs=33.1
Q ss_pred CCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCCCCcccc
Q 047710 22 HPTDEELITYYLLKKVLDCNFTGRAIAEVDLNKCEPWELPAKAK 65 (384)
Q Consensus 22 ~PTDEELI~~YL~~Kv~g~pl~~~~I~evDVY~~ePWdLP~~~~ 65 (384)
|-|..||++.-.+.-..|.|+|. +.|+-+..|.++|+.++
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~ak 90 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAAK 90 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHHH
Confidence 56788888887778888888886 67899999999998764
No 5
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=17.56 E-value=1.3e+02 Score=20.11 Aligned_cols=21 Identities=19% Similarity=0.320 Sum_probs=16.4
Q ss_pred ChHHHHHHHHHhhhcCCCCCC
Q 047710 24 TDEELITYYLLKKVLDCNFTG 44 (384)
Q Consensus 24 TDEELI~~YL~~Kv~g~pl~~ 44 (384)
+-.|||.+|+.-|+.-...++
T Consensus 4 ~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred chHHHHHHHHHHHHhhcCCCC
Confidence 457999999999997665543
No 6
>PF15355 Chisel: Stretch-responsive small skeletal muscle X protein, Chisel
Probab=17.26 E-value=44 Score=27.74 Aligned_cols=15 Identities=33% Similarity=0.698 Sum_probs=13.2
Q ss_pred CCccccccccCccee
Q 047710 315 PNLRSLQENLQLPFF 329 (384)
Q Consensus 315 p~lrs~q~nl~lp~f 329 (384)
+|.|+||-||.+|+=
T Consensus 7 snv~aiQANiNIPMG 21 (87)
T PF15355_consen 7 SNVRAIQANINIPMG 21 (87)
T ss_pred chhHHHHhhcCCccc
Confidence 578999999999983
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=16.68 E-value=99 Score=26.51 Aligned_cols=40 Identities=30% Similarity=0.376 Sum_probs=33.3
Q ss_pred CCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCCCCcccc
Q 047710 22 HPTDEELITYYLLKKVLDCNFTGRAIAEVDLNKCEPWELPAKAK 65 (384)
Q Consensus 22 ~PTDEELI~~YL~~Kv~g~pl~~~~I~evDVY~~ePWdLP~~~~ 65 (384)
|-|..||+|.-.+.-..|.|+|. +-||-+..|.++|..++
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~ak 90 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEAAK 90 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHHHH
Confidence 56788999887778888999887 67899999999997653
No 8
>KOG1214 consensus Nidogen and related basement membrane protein proteins [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=15.84 E-value=66 Score=37.22 Aligned_cols=38 Identities=32% Similarity=0.459 Sum_probs=26.0
Q ss_pred CCCCCCcccccCCCC-C---CCCCC----CCccccccccCcceecc
Q 047710 294 AGAACDPFARFGRNN-V---GLNAF----PNLRSLQENLQLPFFFA 331 (384)
Q Consensus 294 ~~~~~~~~~~~~~~~-~---~~~~f----p~lrs~q~nl~lp~f~~ 331 (384)
-|.+||||.+.-==| + .++.. +.-|-+|+|||.||=+-
T Consensus 1159 NGLtfdpfs~~LCWvDAGt~rleC~~p~g~gRR~i~~~LqYPF~it 1204 (1289)
T KOG1214|consen 1159 NGLTFDPFSKLLCWVDAGTKRLECTLPDGTGRRVIQNNLQYPFSIT 1204 (1289)
T ss_pred CCceeCcccceeeEEecCCcceeEecCCCCcchhhhhcccCceeee
Confidence 489999999864111 1 22222 55688999999999765
No 9
>PF11535 Calci_bind_CcbP: Calcium binding; InterPro: IPR020994 CcbP is a Ca(2+) binding protein found in bacteria which is thought to bind Ca(2+) by protein surface charge. When bound to Ca(2+), the protein becomes more compact and the level of free calcium decreases. Within the bacteria, Ca(2+) has a role in the early stages of heterocyst differentiation. The free Ca(2+) concentration which is regulated by CcbP is critical for the differentiation process []. Calcium signalling is widespread in bacterial species, and prokaryotic cells like eukaryotes are equipped with all the elements to maintain Ca2+ homeostasis [].; PDB: 2P0P_A 2K2V_A 2P0Q_A.
Probab=14.33 E-value=56 Score=28.20 Aligned_cols=10 Identities=60% Similarity=0.996 Sum_probs=7.2
Q ss_pred cccccCccee
Q 047710 320 LQENLQLPFF 329 (384)
Q Consensus 320 ~q~nl~lp~f 329 (384)
|+|+|+|||=
T Consensus 25 Lee~L~fPF~ 34 (106)
T PF11535_consen 25 LEEHLQFPFE 34 (106)
T ss_dssp HHHH--SSEE
T ss_pred HhhhcCCceE
Confidence 8999999996
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=12.96 E-value=1.3e+02 Score=25.78 Aligned_cols=39 Identities=33% Similarity=0.434 Sum_probs=26.2
Q ss_pred CCChHHHHHHHHHhhhcCCCCCCCceeeccCCCCCCCCCCccc
Q 047710 22 HPTDEELITYYLLKKVLDCNFTGRAIAEVDLNKCEPWELPAKA 64 (384)
Q Consensus 22 ~PTDEELI~~YL~~Kv~g~pl~~~~I~evDVY~~ePWdLP~~~ 64 (384)
|-|..||++.-.+.-..|.|+|. +.||-+..|.++|..+
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 57888999887778888999887 6789999999999765
Done!