Query 007598
Match_columns 596
No_of_seqs 211 out of 886
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 12:47:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007598.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007598hhsearch_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 1.1E-40 2.3E-45 300.6 5.4 127 10-138 1-129 (129)
2 PF11669 WBP-1: WW domain-bind 12.4 1.3E+02 0.0028 27.3 1.7 16 572-587 21-36 (102)
3 cd06228 Peptidase_M14-like_3 A 12.3 1.6E+02 0.0034 32.1 2.5 39 518-556 274-316 (332)
4 PF10856 DUF2678: Protein of u 10.9 2.3E+02 0.005 26.9 2.8 19 569-587 91-109 (118)
5 cd00490 Met_repressor_MetJ Met 10.5 2.6E+02 0.0056 25.6 2.9 39 17-59 50-88 (103)
6 cd06248 M14_CPA_CPB_like Pepti 10.5 1.9E+02 0.0042 30.6 2.5 39 517-560 248-287 (304)
7 cd03870 M14_CPA Peptidase M14 10.1 1.2E+02 0.0026 32.2 0.8 38 517-560 243-281 (301)
8 KOG3238 Chloride ion current i 9.6 2.8E+02 0.0061 28.7 3.0 65 7-71 106-170 (216)
9 PRK05264 transcriptional repre 9.2 2.9E+02 0.0062 25.5 2.6 39 17-59 51-89 (105)
10 PF15254 CCDC14: Coiled-coil d 9.1 2.2E+02 0.0047 34.7 2.3 35 470-509 767-801 (861)
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=1.1e-40 Score=300.63 Aligned_cols=127 Identities=53% Similarity=1.038 Sum_probs=97.2
Q ss_pred CCCCceeCCChHHHHHHHHHHhhcCCCCCC-CCeeeccCCCCCCCCCCCcCCcCCCCcceEeeeccccccCCCCCccccc
Q 007598 10 LAPGFRFHPTDEELVRYYLKRKVCHRSLRF-NPICVTDIYKSEPWDLPDKSSLKTRDKEWYFFSMLDKKYGNGSRTNRAT 88 (596)
Q Consensus 10 LPPGFRF~PTDEELV~~YLkrKI~G~plp~-~~I~EvDVY~~ePWdLP~~s~~k~~d~eWYFFSpr~rKy~nG~R~nRat 88 (596)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||++|||+||+. ..+++.+||||+++++++.++.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~--~~~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAK--FKGGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHH--SSS-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhh--ccCCCceEEEEEecccccCCcccccccc
Confidence 899999999999999999999999999888 6899999999999999942 2335679999999999999999999999
Q ss_pred ccceeEecCCcceeec-CCeEEEEEEEEEeeeCCCCCCCCcCeEEEEEEeC
Q 007598 89 EKGYWKTTGKDRPVHH-NTRTVGMKKTLVYHMGRAPHGERTNWVMHEYRLT 138 (596)
Q Consensus 89 ggGyWKatGkdK~I~~-~G~vVG~KKtLvFy~GrapkG~RTdWVMhEYrL~ 138 (596)
++|+||.+|+.++|.. ++.+||+||+|+||.++.+++.+|+|+||||+|.
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 9999999999999988 8999999999999999888899999999999984
No 2
>PF11669 WBP-1: WW domain-binding protein 1; InterPro: IPR021684 This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain [].
Probab=12.44 E-value=1.3e+02 Score=27.31 Aligned_cols=16 Identities=25% Similarity=1.030 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHhhee
Q 007598 572 LWLLLFLWIIILSVGF 587 (596)
Q Consensus 572 ~~~~~f~~~~~l~~s~ 587 (596)
+|+|.++|+||+++++
T Consensus 21 ~w~FWlv~~liill~c 36 (102)
T PF11669_consen 21 LWYFWLVWVLIILLSC 36 (102)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3445567888777654
No 3
>cd06228 Peptidase_M14-like_3 A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly differe
Probab=12.26 E-value=1.6e+02 Score=32.13 Aligned_cols=39 Identities=21% Similarity=0.378 Sum_probs=31.2
Q ss_pred ecCCCccccccc---CCceeEEEEEeeccCCCCCC-CCCCCCC
Q 007598 518 LSGSGLDWSVGK---NGDMNIVFSFDLSQNVISPS-PTSFEPA 556 (596)
Q Consensus 518 ~~~~~~~w~~~k---ng~~~~~~s~~~~~~~~~~~-~~~~~~~ 556 (596)
.+|+++||.++. +|...+.+||++|=++..+. ..||-|.
T Consensus 274 ~sG~s~D~ay~~~~~~~~~~~~~s~t~El~~~~~~~~~gF~~p 316 (332)
T cd06228 274 TSGASDDYAFSRHFADAVKRKVFSYTIEFGETNSEAECPFYPT 316 (332)
T ss_pred CCCChhhhhhhccccccccCceEEEEEEeCCCCCCCCcCCCCC
Confidence 469999999985 78888999999998887643 4588664
No 4
>PF10856 DUF2678: Protein of unknown function (DUF2678); InterPro: IPR022564 This family of proteins has no known function.
Probab=10.88 E-value=2.3e+02 Score=26.92 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=16.5
Q ss_pred hhHHHHHHHHHHHHHhhee
Q 007598 569 FRSLWLLLFLWIIILSVGF 587 (596)
Q Consensus 569 ~r~~~~~~f~~~~~l~~s~ 587 (596)
+|-+.|++++++++|.++-
T Consensus 91 fr~li~~~~~~ivllci~a 109 (118)
T PF10856_consen 91 FRYLIYYNCFSIVLLCICA 109 (118)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 8999999999999987763
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=10.51 E-value=2.6e+02 Score=25.60 Aligned_cols=39 Identities=21% Similarity=0.268 Sum_probs=32.6
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCCCeeeccCCCCCCCCCCCcC
Q 007598 17 HPTDEELVRYYLKRKVCHRSLRFNPICVTDIYKSEPWDLPDKS 59 (596)
Q Consensus 17 ~PTDEELV~~YLkrKI~G~plp~~~I~EvDVY~~ePWdLP~~s 59 (596)
|-|-.||++.-...-..|+|+|. +.|+-+..|..+|...
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 56888888877778889999998 5789999999999754
No 6
>cd06248 M14_CPA_CPB_like Peptidase M14 Carboxypeptidase A/B-like subfamily: This is one of two main M14 carboxypeptidase subfamilies, defined by sequence and structural homology, the other being N/E. Carboxypeptidases (CPs) hydrolyze single, C-terminal amino acids from polypeptide chains. They have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Majority of the proteins in this subfamily have not been characterized as yet. The A/B enzymes are normally synthesized as inactive precursors containing preceding signal peptide, followed by a globular N-terminal pro-region linked to the enzyme; the proenzymes are called procarboxypeptidases. These enzymes exhibit distinct substrate specificity pattern; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. There are nine members in the A/B family: CPA1, CPA2, CPA3, CPA4, CPA5,
Probab=10.46 E-value=1.9e+02 Score=30.59 Aligned_cols=39 Identities=28% Similarity=0.521 Sum_probs=28.3
Q ss_pred eecCCCcccccccCCceeEEEEEeeccCCCCCCCCCCC-CCcccc
Q 007598 517 TLSGSGLDWSVGKNGDMNIVFSFDLSQNVISPSPTSFE-PAGNIF 560 (596)
Q Consensus 517 t~~~~~~~w~~~kng~~~~~~s~~~~~~~~~~~~~~~~-~~~~~~ 560 (596)
+.+|+..||.+++-|. .+||++|=++... -||. |+.+|.
T Consensus 248 ~~~G~~~D~~y~~~gi---~~~~t~El~~~~~--~gf~~p~~~i~ 287 (304)
T cd06248 248 QTTGSSVDWVYHVAGA---AWSYQLELRDTGT--YGFVLPAKQII 287 (304)
T ss_pred cCCCCcchhhhccCCC---cEEEEEEeCCCCC--CCCCCCHHHCc
Confidence 4679999999998774 6777777666544 3897 566654
No 7
>cd03870 M14_CPA Peptidase M14 Carboxypeptidase (CP) A (CPA) belongs to the A/B subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPA enzymes generally favor hydrophobic residues. A/B subfamily enzymes are normally synthesized as inactive precursors containing preceding signal peptide, followed by a globular N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The procarboxypeptidase A (PCPA) is produced by the exocrine pancreas and stored as a stable zymogen in the pancreatic granules until secretion into the digestive tract occurs. This subfamily includes CPA1, CPA2 and CPA4 forms. Within these A forms, there are slightly different specificities, with CPA1 preferring aliphatic and small aromatic residues, and CPA2 p
Probab=10.10 E-value=1.2e+02 Score=32.21 Aligned_cols=38 Identities=32% Similarity=0.578 Sum_probs=27.4
Q ss_pred eecCCCcccccccCCceeEEEEEeeccCCCCCCCCCC-CCCcccc
Q 007598 517 TLSGSGLDWSVGKNGDMNIVFSFDLSQNVISPSPTSF-EPAGNIF 560 (596)
Q Consensus 517 t~~~~~~~w~~~kng~~~~~~s~~~~~~~~~~~~~~~-~~~~~~~ 560 (596)
..+|+..||.+++ .+.+||++|=++..+ .|| =|+.+|.
T Consensus 243 ~a~G~s~Dw~y~~----~~~~s~t~El~~~g~--~gF~lP~~~i~ 281 (301)
T cd03870 243 QASGGSIDWSYNQ----GIKYSFTFELRDTGR--YGFLLPASQII 281 (301)
T ss_pred cCCCChhhhhhcC----CCcEEEEEEeCCCCC--CCCCCChHHCc
Confidence 4679999999975 346788888777644 488 4566655
No 8
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=9.58 E-value=2.8e+02 Score=28.70 Aligned_cols=65 Identities=18% Similarity=0.285 Sum_probs=37.1
Q ss_pred CCCCCCCceeCCChHHHHHHHHHHhhcCCCCCCCCeeeccCCCCCCCCCCCcCCcCCCCcceEee
Q 007598 7 STSLAPGFRFHPTDEELVRYYLKRKVCHRSLRFNPICVTDIYKSEPWDLPDKSSLKTRDKEWYFF 71 (596)
Q Consensus 7 ~~~LPPGFRF~PTDEELV~~YLkrKI~G~plp~~~I~EvDVY~~ePWdLP~~s~~k~~d~eWYFF 71 (596)
......+|||+|+|.--+..---.....+-+-.....+.+-|.-+=|+.-.....+++...||=+
T Consensus 106 dve~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~~~~t~ 170 (216)
T KOG3238|consen 106 DVEPITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSPNSYTY 170 (216)
T ss_pred cccccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCcccccc
Confidence 34567799999999877766333444444333323445566666666665443334444445443
No 9
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=9.21 E-value=2.9e+02 Score=25.49 Aligned_cols=39 Identities=21% Similarity=0.262 Sum_probs=32.4
Q ss_pred CCChHHHHHHHHHHhhcCCCCCCCCeeeccCCCCCCCCCCCcC
Q 007598 17 HPTDEELVRYYLKRKVCHRSLRFNPICVTDIYKSEPWDLPDKS 59 (596)
Q Consensus 17 ~PTDEELV~~YLkrKI~G~plp~~~I~EvDVY~~ePWdLP~~s 59 (596)
|-|-.||++.-...-..|+|+|. +.|+-+..|..+|...
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 56888888876778889999998 5789999999999654
No 10
>PF15254 CCDC14: Coiled-coil domain-containing protein 14
Probab=9.05 E-value=2.2e+02 Score=34.69 Aligned_cols=35 Identities=29% Similarity=0.320 Sum_probs=28.3
Q ss_pred hhccCCCCCcccccCCCChhhhhhccccCCCCCceEEEEe
Q 007598 470 QMLGNVAAAPAFASEFPTKDAALRLNSLAHPSSSVHVTAG 509 (596)
Q Consensus 470 ~~lg~i~appa~asefp~~~~~~~~~s~~~s~~s~~vtag 509 (596)
-.++.|||+. +||...++.+--++-| ++++||..+
T Consensus 767 eai~kiP~~~----~~~~~~~~~~~p~~~~-~~~~~~k~~ 801 (861)
T PF15254_consen 767 EAISKIPAAT----EDPPEQAACHGPSACQ-SSNSQVKGS 801 (861)
T ss_pred hhhccCCCCc----CCCcccccCCCccccc-CCccccccc
Confidence 3788898865 9999999998888866 888999833
Done!