Query 017827
Match_columns 365
No_of_seqs 240 out of 1009
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 03:46:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017827.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017827hhsearch_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 2E-44 4.4E-49 308.8 6.7 127 16-142 1-129 (129)
2 PF02083 Urotensin_II: Urotens 32.5 14 0.00031 20.1 -0.1 7 359-365 4-10 (12)
3 PHA00692 hypothetical protein 22.8 31 0.00067 27.0 0.2 12 13-24 34-45 (74)
4 COG3060 MetJ Transcriptional r 18.2 63 0.0014 27.1 1.1 40 23-66 51-90 (105)
5 cd00933 barnase Barnase, a mem 17.5 3.8E+02 0.0082 23.2 5.7 24 25-51 2-25 (107)
6 cd00490 Met_repressor_MetJ Met 14.9 1.3E+02 0.0027 25.5 2.1 39 23-65 50-88 (103)
7 smart00265 BH4 BH4 Bcl-2 homol 14.9 1.6E+02 0.0035 19.5 2.2 20 25-44 4-23 (27)
8 PF05865 Cypo_polyhedrin: Cypo 14.3 1.4E+02 0.0031 28.0 2.5 28 94-121 140-168 (248)
9 PRK05264 transcriptional repre 13.0 1.4E+02 0.0031 25.3 1.9 39 23-65 51-89 (105)
10 PF07960 CBP4: CBP4; InterPro 12.2 1.1E+02 0.0024 27.2 1.2 17 23-39 30-49 (128)
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=2e-44 Score=308.76 Aligned_cols=127 Identities=59% Similarity=1.128 Sum_probs=98.0
Q ss_pred CCCCceeCCChHHHHHHHHHHhhcCCCCCc-CceecccCCCCCCCCCCccccCCCceEEEEeeccccCCCCCCcccccCC
Q 017827 16 LPPGFRFHPTDEELITHYLYKKVLDVCFSC-RAIGDVDLNKNEPWELPWKAKMGEKEWYFFCMRDRKYPTGLRTNRATVS 94 (365)
Q Consensus 16 LPpGfRF~PTDEELI~~YL~~Kv~g~~~~~-~~I~evDly~~ePWdLP~~a~~GekeWYFFs~r~rKy~~G~R~nRat~~ 94 (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 899999999999999999999999999876 7899999999999999954445677999999999999999999999999
Q ss_pred ceeeecCCCceEee-CCceeEeEEEEEEeeccCCCCCCcCeEEEEEEeC
Q 017827 95 GYWKATGKDKEIYR-GKSLVGMKKTLVFYRGRAPKGEKSSWVMHEYRLD 142 (365)
Q Consensus 95 GyWKatGk~k~I~~-~g~lVG~KKtLvFY~Grapkg~KT~WvMhEYrL~ 142 (365)
|+||++|+.++|.. ++.+||+||+|+||.++.+++.+|+|+||||+|+
T Consensus 81 G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999998 8899999999999999889999999999999984
No 2
>PF02083 Urotensin_II: Urotensin II; InterPro: IPR001483 Urotensin II, a small peptide that contains a disulphide bridge, was originally isolated from the caudal portion of the spinal cord of teleost and elasmobranch fish []. The peptide has also been found in the brain of frogs []. Urotensin II seems to be involved in smooth muscle stimulation.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=32.53 E-value=14 Score=20.14 Aligned_cols=7 Identities=57% Similarity=1.958 Sum_probs=5.4
Q ss_pred CccCCCC
Q 017827 359 FDCFWNY 365 (365)
Q Consensus 359 ~~~~w~~ 365 (365)
.+|||.|
T Consensus 4 ~~CFWKY 10 (12)
T PF02083_consen 4 SECFWKY 10 (12)
T ss_pred cchhhhh
Confidence 4789976
No 3
>PHA00692 hypothetical protein
Probab=22.85 E-value=31 Score=26.99 Aligned_cols=12 Identities=50% Similarity=1.088 Sum_probs=9.3
Q ss_pred CCCCCCCceeCC
Q 017827 13 QMDLPPGFRFHP 24 (365)
Q Consensus 13 ~~~LPpGfRF~P 24 (365)
-...||||||--
T Consensus 34 fveyppgfrfgg 45 (74)
T PHA00692 34 FVEYPPGFRFGG 45 (74)
T ss_pred eEecCCCccccc
Confidence 357899999963
No 4
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=18.25 E-value=63 Score=27.08 Aligned_cols=40 Identities=30% Similarity=0.381 Sum_probs=33.3
Q ss_pred CCChHHHHHHHHHHhhcCCCCCcCceecccCCCCCCCCCCcccc
Q 017827 23 HPTDEELITHYLYKKVLDVCFSCRAIGDVDLNKNEPWELPWKAK 66 (365)
Q Consensus 23 ~PTDEELI~~YL~~Kv~g~~~~~~~I~evDly~~ePWdLP~~a~ 66 (365)
|-|.-||+|.-...-..|+|+| .+.|+-+.-|-++|+.++
T Consensus 51 hatnsellceaflhaftgqplp----td~dl~ker~deipe~ak 90 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLP----TDADLRKERSDEIPEAAK 90 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCC----CcHHHHHhccccchHHHH
Confidence 6788899887777888999987 467999999999998764
No 5
>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=17.51 E-value=3.8e+02 Score=23.22 Aligned_cols=24 Identities=13% Similarity=0.087 Sum_probs=15.3
Q ss_pred ChHHHHHHHHHHhhcCCCCCcCceecc
Q 017827 25 TDEELITHYLYKKVLDVCFSCRAIGDV 51 (365)
Q Consensus 25 TDEELI~~YL~~Kv~g~~~~~~~I~ev 51 (365)
|+.|-|..||.. .+ .+|..+|.-.
T Consensus 2 ~~~~~V~~y~~~--~~-~LP~~yiTK~ 25 (107)
T cd00933 2 NTFQGVADYLQT--YH-RLPDNYITKS 25 (107)
T ss_pred chHHHHHHHHHH--hC-cCCcceEeHH
Confidence 455667789977 33 3777777654
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=14.92 E-value=1.3e+02 Score=25.48 Aligned_cols=39 Identities=28% Similarity=0.345 Sum_probs=32.9
Q ss_pred CCChHHHHHHHHHHhhcCCCCCcCceecccCCCCCCCCCCccc
Q 017827 23 HPTDEELITHYLYKKVLDVCFSCRAIGDVDLNKNEPWELPWKA 65 (365)
Q Consensus 23 ~PTDEELI~~YL~~Kv~g~~~~~~~I~evDly~~ePWdLP~~a 65 (365)
|-|--||+|.-...-..|+|+|. +-||-+..|-++|+.+
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 67888999887778889999984 6789999999999765
No 7
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=14.87 E-value=1.6e+02 Score=19.52 Aligned_cols=20 Identities=20% Similarity=0.405 Sum_probs=15.7
Q ss_pred ChHHHHHHHHHHhhcCCCCC
Q 017827 25 TDEELITHYLYKKVLDVCFS 44 (365)
Q Consensus 25 TDEELI~~YL~~Kv~g~~~~ 44 (365)
.-.|||.+|+.-|+.-+..+
T Consensus 4 ~nRelV~~yv~yKLsQrgy~ 23 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGYE 23 (27)
T ss_pred chHHHHHHHHHHHHhhcCCC
Confidence 45799999999999766543
No 8
>PF05865 Cypo_polyhedrin: Cypovirus polyhedrin protein; InterPro: IPR008464 This family consists of several Cypovirus polyhedrin proteins. Polyhedrin is known to form a crystalline matrix (polyhedra) in infected insect cells [].; PDB: 2OH7_A 2OH5_A 2OH6_A.
Probab=14.32 E-value=1.4e+02 Score=27.98 Aligned_cols=28 Identities=32% Similarity=0.549 Sum_probs=18.2
Q ss_pred CceeeecCCC-ceEeeCCceeEeEEEEEE
Q 017827 94 SGYWKATGKD-KEIYRGKSLVGMKKTLVF 121 (365)
Q Consensus 94 ~GyWKatGk~-k~I~~~g~lVG~KKtLvF 121 (365)
+--|.+||-. |.|..+|++||+...|..
T Consensus 140 shpweatgikyrki~~dgeivgyshyfel 168 (248)
T PF05865_consen 140 SHPWEATGIKYRKIHRDGEIVGYSHYFEL 168 (248)
T ss_dssp --S-B--GGG-EEEEETTEEEEEEEEEE-
T ss_pred cCCccccCceEEEeeccceEeeeeeeeec
Confidence 3459999865 778889999999887643
No 9
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=13.00 E-value=1.4e+02 Score=25.33 Aligned_cols=39 Identities=28% Similarity=0.328 Sum_probs=32.7
Q ss_pred CCChHHHHHHHHHHhhcCCCCCcCceecccCCCCCCCCCCccc
Q 017827 23 HPTDEELITHYLYKKVLDVCFSCRAIGDVDLNKNEPWELPWKA 65 (365)
Q Consensus 23 ~PTDEELI~~YL~~Kv~g~~~~~~~I~evDly~~ePWdLP~~a 65 (365)
|-|--||+|.-...-..|+|+|. +-||-+..|-++|+.+
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 67888999887778889999984 6789999999999765
No 10
>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=12.18 E-value=1.1e+02 Score=27.19 Aligned_cols=17 Identities=53% Similarity=0.866 Sum_probs=12.5
Q ss_pred CCChHHHHHHH---HHHhhc
Q 017827 23 HPTDEELITHY---LYKKVL 39 (365)
Q Consensus 23 ~PTDEELI~~Y---L~~Kv~ 39 (365)
.||||||+..| |+++.+
T Consensus 30 tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 30 TPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred CCCHHHHHHhcCHHHHHHHH
Confidence 49999999876 455544
Done!