Query 036998
Match_columns 265
No_of_seqs 152 out of 964
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 07:32:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036998hhsearch_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 3E-43 6.5E-48 288.0 5.9 127 6-134 1-129 (129)
2 COG4741 Predicted secreted end 36.0 15 0.00032 31.7 0.5 16 1-18 95-110 (175)
3 PHA00692 hypothetical protein 29.3 20 0.00044 25.9 0.2 10 5-14 36-45 (74)
4 smart00265 BH4 BH4 Bcl-2 homol 27.1 74 0.0016 19.4 2.4 19 15-33 4-22 (27)
5 cd00490 Met_repressor_MetJ Met 24.8 72 0.0016 25.0 2.6 38 13-54 50-87 (103)
6 KOG3238 Chloride ion current i 22.9 90 0.0019 28.0 3.1 47 6-52 109-155 (216)
7 PRK05264 transcriptional repre 22.6 77 0.0017 25.0 2.4 38 13-54 51-88 (105)
8 COG3060 MetJ Transcriptional r 21.9 60 0.0013 25.3 1.6 39 13-55 51-89 (105)
9 PF01340 MetJ: Met Apo-repress 19.4 1E+02 0.0023 24.1 2.5 38 13-54 50-87 (104)
10 PF10107 Endonuc_Holl: Endonuc 15.5 54 0.0012 28.1 0.1 15 1-17 82-96 (156)
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=3e-43 Score=288.01 Aligned_cols=127 Identities=56% Similarity=1.135 Sum_probs=96.5
Q ss_pred CCCCceECCChHHHHHHHHHHHHcCCCCCC-CceeeccCCCCCCCCCCccCCCCCCCceEEeeccCCCCCCCCCCcceec
Q 036998 6 LPPGFRFHPTDEELVAYYLDRKINGRTIEL-EIIPEIDLYKHEPWDLPDKSYLPGKDMEWYFFSPRDKKYPNGSRTNRAT 84 (265)
Q Consensus 6 LPpGfRF~PTDeELV~~YL~~Ki~G~pl~~-~~I~e~DVY~~~PwdLp~~~~~~~~d~~wYFFs~r~~k~~~G~R~~R~t 84 (265)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+|++.. .+.+.+||||+++++++.++.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~--~~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKF--KGGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHS--SS-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhc--cCCCceEEEEEecccccCCcccccccc
Confidence 899999999999999999999999999887 79999999999999999432 235669999999999999999999999
Q ss_pred cCceeeecCCCeEEec-CccceeeEEEEEeecCCCCCCCCcCeEEEEEEeC
Q 036998 85 RAGYWKATGKDRTVHS-HKQSVGMKKTLVYYRGRAPHGIRTNWVMHEYRLL 134 (265)
Q Consensus 85 ~gG~Wk~~G~~k~I~~-~~~~VG~KrtL~Fy~g~~~~g~kT~W~M~EY~l~ 134 (265)
++|+||.+|+.+.|.+ ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 9999999999999998 8899999999999998888899999999999984
No 2
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=36.04 E-value=15 Score=31.66 Aligned_cols=16 Identities=38% Similarity=0.962 Sum_probs=12.4
Q ss_pred CCCCCCCCCceECCChHH
Q 036998 1 MAPMSLPPGFRFHPTDEE 18 (265)
Q Consensus 1 ~ap~~LPpGfRF~PTDeE 18 (265)
|||+ -|+|+|+|.|.-
T Consensus 95 laPf--fp~f~ynPkD~R 110 (175)
T COG4741 95 LAPF--FPEFKYNPKDAR 110 (175)
T ss_pred hccc--ccCCCcCCccce
Confidence 6777 459999999853
No 3
>PHA00692 hypothetical protein
Probab=29.26 E-value=20 Score=25.93 Aligned_cols=10 Identities=60% Similarity=1.255 Sum_probs=7.9
Q ss_pred CCCCCceECC
Q 036998 5 SLPPGFRFHP 14 (265)
Q Consensus 5 ~LPpGfRF~P 14 (265)
..||||||--
T Consensus 36 eyppgfrfgg 45 (74)
T PHA00692 36 EYPPGFRFGG 45 (74)
T ss_pred ecCCCccccc
Confidence 5699999963
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=27.09 E-value=74 Score=19.42 Aligned_cols=19 Identities=26% Similarity=0.406 Sum_probs=15.1
Q ss_pred ChHHHHHHHHHHHHcCCCC
Q 036998 15 TDEELVAYYLDRKINGRTI 33 (265)
Q Consensus 15 TDeELV~~YL~~Ki~G~pl 33 (265)
+-.|||.+|+.-|+.-+..
T Consensus 4 ~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 4 DNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred chHHHHHHHHHHHHhhcCC
Confidence 4579999999999975543
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=24.81 E-value=72 Score=24.98 Aligned_cols=38 Identities=24% Similarity=0.403 Sum_probs=30.5
Q ss_pred CCChHHHHHHHHHHHHcCCCCCCCceeeccCCCCCCCCCCcc
Q 036998 13 HPTDEELVAYYLDRKINGRTIELEIIPEIDLYKHEPWDLPDK 54 (265)
Q Consensus 13 ~PTDeELV~~YL~~Ki~G~pl~~~~I~e~DVY~~~PwdLp~~ 54 (265)
|-|-.||++.-...-..|+|||. +.|+-...|.++|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHH
Confidence 45778998876677789999994 578888899999865
No 6
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=22.88 E-value=90 Score=27.97 Aligned_cols=47 Identities=19% Similarity=0.306 Sum_probs=24.9
Q ss_pred CCCCceECCChHHHHHHHHHHHHcCCCCCCCceeeccCCCCCCCCCC
Q 036998 6 LPPGFRFHPTDEELVAYYLDRKINGRTIELEIIPEIDLYKHEPWDLP 52 (265)
Q Consensus 6 LPpGfRF~PTDeELV~~YL~~Ki~G~pl~~~~I~e~DVY~~~PwdLp 52 (265)
.--+|||+|+|.--+...--....+.-+-+....+.+-|.-+=|+.-
T Consensus 109 ~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~me 155 (216)
T KOG3238|consen 109 PITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDME 155 (216)
T ss_pred ccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhh
Confidence 34589999999877764222323333222222334455555555543
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=22.64 E-value=77 Score=24.97 Aligned_cols=38 Identities=24% Similarity=0.386 Sum_probs=30.3
Q ss_pred CCChHHHHHHHHHHHHcCCCCCCCceeeccCCCCCCCCCCcc
Q 036998 13 HPTDEELVAYYLDRKINGRTIELEIIPEIDLYKHEPWDLPDK 54 (265)
Q Consensus 13 ~PTDeELV~~YL~~Ki~G~pl~~~~I~e~DVY~~~PwdLp~~ 54 (265)
|-|-.||++.-...-..|+|||. +.|+-...|.++|..
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~ 88 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEA 88 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHH
Confidence 45778998876677789999994 578888899999864
No 8
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=21.94 E-value=60 Score=25.26 Aligned_cols=39 Identities=23% Similarity=0.437 Sum_probs=30.7
Q ss_pred CCChHHHHHHHHHHHHcCCCCCCCceeeccCCCCCCCCCCccC
Q 036998 13 HPTDEELVAYYLDRKINGRTIELEIIPEIDLYKHEPWDLPDKS 55 (265)
Q Consensus 13 ~PTDeELV~~YL~~Ki~G~pl~~~~I~e~DVY~~~PwdLp~~~ 55 (265)
|-|..||++.-...-..|+||| .+.|+...-|.++|...
T Consensus 51 hatnsellceaflhaftgqplp----td~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLP----TDADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCC----CcHHHHHhccccchHHH
Confidence 4577888887667778999998 45788888889998753
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=19.37 E-value=1e+02 Score=24.13 Aligned_cols=38 Identities=26% Similarity=0.451 Sum_probs=23.8
Q ss_pred CCChHHHHHHHHHHHHcCCCCCCCceeeccCCCCCCCCCCcc
Q 036998 13 HPTDEELVAYYLDRKINGRTIELEIIPEIDLYKHEPWDLPDK 54 (265)
Q Consensus 13 ~PTDeELV~~YL~~Ki~G~pl~~~~I~e~DVY~~~PwdLp~~ 54 (265)
|-|..||++.-...-..|+|||. +.|+-...|..+|..
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~----D~dl~kd~~d~ip~~ 87 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT----DDDLRKDRPDEIPAE 87 (104)
T ss_dssp S-SHHHHHHHHHHHHHH----------TTGGGSTSGSSS-HH
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCCccchHH
Confidence 45788998876667789999984 478888899998864
No 10
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase; InterPro: IPR019287 This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=15.50 E-value=54 Score=28.13 Aligned_cols=15 Identities=40% Similarity=0.970 Sum_probs=12.5
Q ss_pred CCCCCCCCCceECCChH
Q 036998 1 MAPMSLPPGFRFHPTDE 17 (265)
Q Consensus 1 ~ap~~LPpGfRF~PTDe 17 (265)
|||+ -|+|.|+|+|.
T Consensus 82 laP~--lp~F~ynP~D~ 96 (156)
T PF10107_consen 82 LAPF--LPEFPYNPKDA 96 (156)
T ss_pred hhhc--cCCCCCChhhh
Confidence 5777 49999999985
Done!