Query 023197
Match_columns 286
No_of_seqs 185 out of 985
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:09:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023197.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023197hhsearch_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 3.6E-45 7.7E-50 303.4 6.2 127 9-135 1-129 (129)
2 COG3670 Lignostilbene-alpha,be 24.5 51 0.0011 33.8 2.2 43 122-164 409-451 (490)
3 PHA00692 hypothetical protein 24.1 31 0.00066 25.7 0.4 9 8-16 36-44 (74)
4 PF09174 Maf1: Maf1 regulator; 20.6 28 0.00062 30.7 -0.4 12 41-52 137-148 (179)
5 cd00490 Met_repressor_MetJ Met 20.1 84 0.0018 25.2 2.1 39 16-58 50-88 (103)
6 smart00265 BH4 BH4 Bcl-2 homol 18.2 1.3E+02 0.0028 18.9 2.2 19 18-36 4-22 (27)
7 PRK05264 transcriptional repre 17.9 92 0.002 25.1 1.9 39 16-58 51-89 (105)
8 PF12672 DUF3793: Protein of u 17.5 82 0.0018 27.7 1.8 38 12-55 83-121 (176)
9 PF07960 CBP4: CBP4; InterPro 17.4 67 0.0015 27.3 1.1 11 16-26 30-40 (128)
10 PF04700 Baculo_gp41: Structur 17.2 1.2E+02 0.0026 27.3 2.7 21 18-38 6-28 (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=3.6e-45 Score=303.39 Aligned_cols=127 Identities=61% Similarity=1.191 Sum_probs=98.1
Q ss_pred CCCCceeCCChHHHHHHHHHHhhcCCCCCC-cceeeccCCCCCCCCCCccccCCceeEEEeecCCCCCCCCCCCcccccC
Q 023197 9 LPPGFRFHPTDEELIVHYLRNQATSRPCPV-SIIPEVDIYKFDPWQLPEKAEFGEKEWYFFSPRDRKYPNGTRPNRATVS 87 (286)
Q Consensus 9 LPpGfRF~PTDEELI~~YL~~Ki~g~p~p~-~iI~evDVY~~~PweLp~~~~~ge~eWYFFt~r~rk~~nG~R~~R~~g~ 87 (286)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+||+....++++||||+++++++.+|.|++|++++
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 7999999999999999965455678999999999999999999999999
Q ss_pred CeEEecccCceEec-CCeeeeeEEEEEEeeCCCCCCCCcCeeEeeeeeC
Q 023197 88 GYWKATGTDKAIYG-GSKYLGVKKALVFYKGRPPKGIKTDWIMHEYRLN 135 (286)
Q Consensus 88 G~WKatG~~k~I~~-~g~~VG~KktL~Fy~g~~p~g~kT~WiMhEY~L~ 135 (286)
|+||++|+.+.|.+ ++.+||+|++|+||.++.+++.+|+|+||||+|.
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 8899999999999999888999999999999984
No 2
>COG3670 Lignostilbene-alpha,beta-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.45 E-value=51 Score=33.75 Aligned_cols=43 Identities=14% Similarity=0.217 Sum_probs=22.8
Q ss_pred CCCcCeeEeeeeeCCCCCCCCCCCCCCCCCcEEEEEEEeeCCC
Q 023197 122 GIKTDWIMHEYRLNDPTRQPYKHNGSMKLDDWVLCRIYKKRQT 164 (286)
Q Consensus 122 g~kT~WiMhEY~L~~~~~~~~~~~~~~~~~d~VLCRIy~k~~~ 164 (286)
|..+.|.--|=++........+...+.+.+-|+||-||.-.+.
T Consensus 409 g~~~~~~~g~~~y~~E~vfvPrpg~~~EdDGwLl~~vyd~~~~ 451 (490)
T COG3670 409 GTSQVYSFGPRGYGSEPVFVPRPGSSAEDDGWLLTLVYDGDRH 451 (490)
T ss_pred CcEEEEecCCCCcccccccccCCCCCcCCCcEEEEEEEecCCC
Confidence 3344343333333333333333334456788999999976433
No 3
>PHA00692 hypothetical protein
Probab=24.05 E-value=31 Score=25.66 Aligned_cols=9 Identities=78% Similarity=1.578 Sum_probs=7.5
Q ss_pred CCCCCceeC
Q 023197 8 ELPPGFRFH 16 (286)
Q Consensus 8 ~LPpGfRF~ 16 (286)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 579999994
No 4
>PF09174 Maf1: Maf1 regulator; InterPro: IPR015257 Maf1 is a negative regulator of RNA polymerase III [, ]. It targets the initiation factor TFIIIB []. ; PDB: 3NR5_A.
Probab=20.62 E-value=28 Score=30.67 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=6.9
Q ss_pred eeeccCCCCCCC
Q 023197 41 IPEVDIYKFDPW 52 (286)
Q Consensus 41 I~evDVY~~~Pw 52 (286)
+.+||||.+.|.
T Consensus 137 l~~C~iYsy~pd 148 (179)
T PF09174_consen 137 LKDCDIYSYNPD 148 (179)
T ss_dssp GGG-EEEEE---
T ss_pred ccCceEEEEccC
Confidence 568899999984
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=20.12 E-value=84 Score=25.22 Aligned_cols=39 Identities=31% Similarity=0.462 Sum_probs=31.4
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCcceeeccCCCCCCCCCCccc
Q 023197 16 HPTDEELIVHYLRNQATSRPCPVSIIPEVDIYKFDPWQLPEKA 58 (286)
Q Consensus 16 ~PTDEELI~~YL~~Ki~g~p~p~~iI~evDVY~~~PweLp~~~ 58 (286)
|-|.-||+..-...-..|+|+|. +.|+-+..|.++|+.+
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 56777887776667789999996 6789999999999765
No 6
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=18.18 E-value=1.3e+02 Score=18.87 Aligned_cols=19 Identities=21% Similarity=0.445 Sum_probs=15.0
Q ss_pred ChHHHHHHHHHHhhcCCCC
Q 023197 18 TDEELIVHYLRNQATSRPC 36 (286)
Q Consensus 18 TDEELI~~YL~~Ki~g~p~ 36 (286)
+-.|||.+|+.-|+.-+..
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999875543
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=17.92 E-value=92 Score=25.14 Aligned_cols=39 Identities=31% Similarity=0.445 Sum_probs=31.3
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCcceeeccCCCCCCCCCCccc
Q 023197 16 HPTDEELIVHYLRNQATSRPCPVSIIPEVDIYKFDPWQLPEKA 58 (286)
Q Consensus 16 ~PTDEELI~~YL~~Ki~g~p~p~~iI~evDVY~~~PweLp~~~ 58 (286)
|-|--||+..-...-..|+|+|. +-|+-+..|.++|+.+
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 56777887776666789999996 6789999999999764
No 8
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=17.46 E-value=82 Score=27.72 Aligned_cols=38 Identities=18% Similarity=0.311 Sum_probs=24.5
Q ss_pred CceeCCChHHHHHHHHHHhhcCCCCCCcceeeccCC-CCCCCCCC
Q 023197 12 GFRFHPTDEELIVHYLRNQATSRPCPVSIIPEVDIY-KFDPWQLP 55 (286)
Q Consensus 12 GfRF~PTDEELI~~YL~~Ki~g~p~p~~iI~evDVY-~~~PweLp 55 (286)
|| .+.+-+-+...|+.|..+..+| ||+=|+ ++...|.-
T Consensus 83 GY--~~~~~~~~L~~L~~R~~~~~FP----HEIGiFLGYPleDV~ 121 (176)
T PF12672_consen 83 GY--PDSSLEDCLEHLKKRFESGEFP----HEIGIFLGYPLEDVK 121 (176)
T ss_pred Cc--CCCCHHHHHHHHHHHhcCCCCC----chhHhccCCCHHHHH
Confidence 66 5556555556688888766677 466665 56666653
No 9
>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=17.42 E-value=67 Score=27.27 Aligned_cols=11 Identities=55% Similarity=0.951 Sum_probs=9.8
Q ss_pred CCChHHHHHHH
Q 023197 16 HPTDEELIVHY 26 (286)
Q Consensus 16 ~PTDEELI~~Y 26 (286)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 69999999886
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=17.22 E-value=1.2e+02 Score=27.32 Aligned_cols=21 Identities=38% Similarity=0.550 Sum_probs=13.9
Q ss_pred ChHHHHHHH--HHHhhcCCCCCC
Q 023197 18 TDEELIVHY--LRNQATSRPCPV 38 (286)
Q Consensus 18 TDEELI~~Y--L~~Ki~g~p~p~ 38 (286)
+|||||.|| |.++..|...+.
T Consensus 6 sDe~Li~yY~~L~K~~g~~~~~~ 28 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGSDVPS 28 (186)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCc
Confidence 788888888 455555554443
Done!