Query 025053
Match_columns 258
No_of_seqs 136 out of 970
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 09:38:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025053.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025053hhsearch_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 6E-38 1.3E-42 255.9 8.7 125 20-161 1-129 (129)
2 PF07131 DUF1382: Protein of u 23.0 84 0.0018 22.9 2.5 21 22-42 22-49 (61)
3 PF07960 CBP4: CBP4; InterPro 21.4 64 0.0014 26.9 1.8 17 26-42 29-49 (128)
4 PHA00692 hypothetical protein 21.3 32 0.00069 25.1 0.0 18 11-28 28-45 (74)
5 PLN02417 dihydrodipicolinate s 19.0 64 0.0014 29.5 1.5 31 11-42 94-124 (280)
6 PF13822 ACC_epsilon: Acyl-CoA 17.5 65 0.0014 23.1 1.0 10 26-35 9-18 (62)
7 PRK14372 hypothetical protein; 17.2 38 0.00083 26.9 -0.3 28 1-32 1-28 (97)
8 cd00952 CHBPH_aldolase Trans-o 15.7 85 0.0018 29.2 1.5 29 12-41 102-130 (309)
9 COG5628 Predicted acetyltransf 13.5 2.2E+02 0.0047 23.9 3.2 48 111-164 29-77 (143)
10 PF12672 DUF3793: Protein of u 13.5 83 0.0018 27.2 0.8 39 23-75 83-122 (176)
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=6e-38 Score=255.94 Aligned_cols=125 Identities=41% Similarity=0.710 Sum_probs=88.5
Q ss_pred CCCceeeCCChHHHHH-HHHHHHhcCcCCCCCccc-ccccccccccCcCCCCCCCCCcc-ccCCceEEEEecCCCCCCCC
Q 025053 20 LPAGVKFDPTDQELLE-HLEAKVRADARKLHPLID-EFIPTLEGENGICYTHPEKLPGV-SKDGLIRHFFHRPSKAYTTG 96 (258)
Q Consensus 20 LPpGfRF~PTDeELI~-yL~~Kv~g~~~~~~Pl~~-~~I~~vd~e~DVY~~~PweLp~~-~~~g~~~yFF~~~~kk~~~G 96 (258)
|||||||+|||+|||. ||++|+.|.. ++. .+|+ ++|||++|||+||.. ...++.||||+++.+++.+|
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~-----~~~~~~i~----~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~ 71 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEP-----LPCEDVIH----DVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNG 71 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-H-----HCS-CHSE----E--GGGS-GGGCHHHSSS-SSEEEEEEE--------
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCC-----CCccccee----ecccCccChHHhhhhccCCCceEEEEEecccccCCc
Confidence 8999999999999996 6999999954 333 4564 457999999999943 23456899999998888889
Q ss_pred CcccccccccCCCCCceEeecCCCceEEe-CCeEEEEEEEEEEEeecCCCCCCCccceEEEEEeeC
Q 025053 97 TRKRRKVHTDEQGGETRWHKTGKTRPVFI-GGKVKGYKKILVLYTNYGKQKKPEKTNWVMHQYHLG 161 (258)
Q Consensus 97 ~R~~R~~~~~~~gg~G~Wk~~G~~k~I~~-~G~vvG~Kk~l~Fy~~~g~~~~g~kT~WvMhEY~L~ 161 (258)
.|++|++ ++|+||++|+.++|.+ +|.++|+|++|+||. ++.+++.+|+|+||||+|.
T Consensus 72 ~r~~R~~------~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~--~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 72 GRPNRVT------GGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYS--GKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp --S-EEE------TTEEEEEECEEEEEEE-TTCEEEEEEEEEEEE--SSTTS-EEEEEEEEEEEE-
T ss_pred ccccccc------cceEEeecccccccccccceeeeeEEEEEEEe--ccCCCCCcCCeEEEEEEeC
Confidence 9999975 3799999999999999 999999999999998 7788999999999999984
No 2
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=23.04 E-value=84 Score=22.89 Aligned_cols=21 Identities=38% Similarity=0.687 Sum_probs=15.2
Q ss_pred CceeeCC----ChHHHHHH---HHHHHh
Q 025053 22 AGVKFDP----TDQELLEH---LEAKVR 42 (258)
Q Consensus 22 pGfRF~P----TDeELI~y---L~~Kv~ 42 (258)
.|+||.| ||+|.... |..|+-
T Consensus 22 ~GIRFVpiPv~~dee~~~L~s~~~~kLe 49 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHTLSSQLSQKLE 49 (61)
T ss_pred cCceeeccccccHHHHHHHHHHHHHHHH
Confidence 4999999 78887642 666654
No 3
>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=21.38 E-value=64 Score=26.90 Aligned_cols=17 Identities=29% Similarity=0.477 Sum_probs=12.4
Q ss_pred eCCChHHHHH-H---HHHHHh
Q 025053 26 FDPTDQELLE-H---LEAKVR 42 (258)
Q Consensus 26 F~PTDeELI~-y---L~~Kv~ 42 (258)
=.||||||+. | |+.+..
T Consensus 29 ~tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 29 TTPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred cCCCHHHHHHhcCHHHHHHHH
Confidence 3799999995 4 666554
No 4
>PHA00692 hypothetical protein
Probab=21.25 E-value=32 Score=25.11 Aligned_cols=18 Identities=28% Similarity=0.564 Sum_probs=12.7
Q ss_pred hhcccCCCCCCCceeeCC
Q 025053 11 KARIHDLPGLPAGVKFDP 28 (258)
Q Consensus 11 ~~~~~~~~~LPpGfRF~P 28 (258)
..+-+.....||||||--
T Consensus 28 edrthyfveyppgfrfgg 45 (74)
T PHA00692 28 EDRTHYFVEYPPGFRFGG 45 (74)
T ss_pred ccceeEeEecCCCccccc
Confidence 334455667899999964
No 5
>PLN02417 dihydrodipicolinate synthase
Probab=18.96 E-value=64 Score=29.49 Aligned_cols=31 Identities=13% Similarity=0.214 Sum_probs=21.7
Q ss_pred hhcccCCCCCCCceeeCCChHHHHHHHHHHHh
Q 025053 11 KARIHDLPGLPAGVKFDPTDQELLEHLEAKVR 42 (258)
Q Consensus 11 ~~~~~~~~~LPpGfRF~PTDeELI~yL~~Kv~ 42 (258)
+.+.....-+|| +.|.||++||+.|++.-+.
T Consensus 94 ~~Gadav~~~~P-~y~~~~~~~i~~~f~~va~ 124 (280)
T PLN02417 94 AVGMHAALHINP-YYGKTSQEGLIKHFETVLD 124 (280)
T ss_pred HcCCCEEEEcCC-ccCCCCHHHHHHHHHHHHh
Confidence 445555555677 5689999999999864433
No 6
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=17.53 E-value=65 Score=23.12 Aligned_cols=10 Identities=50% Similarity=0.664 Sum_probs=8.1
Q ss_pred eCCChHHHHH
Q 025053 26 FDPTDQELLE 35 (258)
Q Consensus 26 F~PTDeELI~ 35 (258)
=+||||||--
T Consensus 9 GnPt~eElAA 18 (62)
T PF13822_consen 9 GNPTDEELAA 18 (62)
T ss_pred CCCCHHHHHH
Confidence 3899999963
No 7
>PRK14372 hypothetical protein; Provisional
Probab=17.18 E-value=38 Score=26.90 Aligned_cols=28 Identities=32% Similarity=0.632 Sum_probs=20.7
Q ss_pred CEEeeeechhhhcccCCCCCCCceeeCCChHH
Q 025053 1 MVIMIRWPFFKARIHDLPGLPAGVKFDPTDQE 32 (258)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~LPpGfRF~PTDeE 32 (258)
|+.+||+ -|..++.+ +++-+||.||=-|
T Consensus 1 ~i~lIr~--YQ~~iSPl--~g~~CRf~PTCS~ 28 (97)
T PRK14372 1 MIRGIRW--YQQRISAN--TPPCCKYYPSCSN 28 (97)
T ss_pred CcHHHHH--HHHHhCCC--CCCCCCcCccHHH
Confidence 5666664 67777665 6799999999655
No 8
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=15.74 E-value=85 Score=29.22 Aligned_cols=29 Identities=0% Similarity=-0.225 Sum_probs=21.5
Q ss_pred hcccCCCCCCCceeeCCChHHHHHHHHHHH
Q 025053 12 ARIHDLPGLPAGVKFDPTDQELLEHLEAKV 41 (258)
Q Consensus 12 ~~~~~~~~LPpGfRF~PTDeELI~yL~~Kv 41 (258)
.|....+-+|| +.|.||++||++|++.=+
T Consensus 102 ~Gad~vlv~~P-~y~~~~~~~l~~yf~~va 130 (309)
T cd00952 102 LGADGTMLGRP-MWLPLDVDTAVQFYRDVA 130 (309)
T ss_pred hCCCEEEECCC-cCCCCCHHHHHHHHHHHH
Confidence 45555666777 679999999999986443
No 9
>COG5628 Predicted acetyltransferase [General function prediction only]
Probab=13.55 E-value=2.2e+02 Score=23.90 Aligned_cols=48 Identities=19% Similarity=0.393 Sum_probs=36.0
Q ss_pred CceEeecCCCceEEe-CCeEEEEEEEEEEEeecCCCCCCCccceEEEEEeeCCCC
Q 025053 111 ETRWHKTGKTRPVFI-GGKVKGYKKILVLYTNYGKQKKPEKTNWVMHQYHLGGNE 164 (258)
Q Consensus 111 ~G~Wk~~G~~k~I~~-~G~vvG~Kk~l~Fy~~~g~~~~g~kT~WvMhEY~L~~~~ 164 (258)
+.+|+..+..--.+. +|.+||+--.| .+.....+.+|.|-||-+...-
T Consensus 29 ~~~w~~~~~~~~~~~~~~~~igf~l~L------~~~~~~~~iD~~~~efFIi~k~ 77 (143)
T COG5628 29 ETYWRDPVREAWLFRIGGLPVGFALVL------DLAHSPTPIDRAVAEFFIVRKH 77 (143)
T ss_pred hhhhcCcccceeEEEECCceeeeeeee------cccCCCCcccccchheEeeehh
Confidence 458888776554444 89999987666 4456678899999999988754
No 10
>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=13.54 E-value=83 Score=27.16 Aligned_cols=39 Identities=28% Similarity=0.353 Sum_probs=23.8
Q ss_pred ceeeCCChHHHHHHHHHHHhcCcCCCCCcccccccccccccCcC-CCCCCCCCc
Q 025053 23 GVKFDPTDQELLEHLEAKVRADARKLHPLIDEFIPTLEGENGIC-YTHPEKLPG 75 (258)
Q Consensus 23 GfRF~PTDeELI~yL~~Kv~g~~~~~~Pl~~~~I~~vd~e~DVY-~~~PweLp~ 75 (258)
|| ..-+-++++.+|..|+.... .| ||+.|. +++..|.-+
T Consensus 83 GY-~~~~~~~~L~~L~~R~~~~~-----FP--------HEIGiFLGYPleDV~G 122 (176)
T PF12672_consen 83 GY-PDSSLEDCLEHLKKRFESGE-----FP--------HEIGIFLGYPLEDVKG 122 (176)
T ss_pred Cc-CCCCHHHHHHHHHHHhcCCC-----CC--------chhHhccCCCHHHHHH
Confidence 77 55556777789999984421 22 344454 667666544
Done!