Query 016435
Match_columns 389
No_of_seqs 134 out of 873
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:49:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016435.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016435hhsearch_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 9E-42 1.9E-46 294.3 5.2 128 3-134 1-129 (129)
2 PHA00692 hypothetical protein 27.2 23 0.0005 28.1 0.2 9 2-10 36-44 (74)
3 PF08483 IstB_IS21_ATP: IstB-l 15.8 1.1E+02 0.0025 20.9 1.7 19 365-383 10-28 (30)
4 KOG3238 Chloride ion current i 14.4 1.3E+02 0.0028 29.2 2.4 62 4-65 110-171 (216)
5 COG5450 Transcription regulato 13.6 76 0.0017 26.6 0.5 25 260-284 52-76 (84)
6 PLN02417 dihydrodipicolinate s 11.7 1.2E+02 0.0026 29.7 1.3 18 3-21 103-120 (280)
7 cd00952 CHBPH_aldolase Trans-o 11.4 1.2E+02 0.0027 30.1 1.3 18 2-20 109-126 (309)
8 KOG2590 RNA-binding protein LA 10.8 1.3E+02 0.0028 32.4 1.2 26 363-388 330-355 (448)
9 PF07960 CBP4: CBP4; InterPro 10.6 1.3E+02 0.0029 27.0 1.1 11 10-20 30-40 (128)
10 cd00954 NAL N-Acetylneuraminic 10.5 1.3E+02 0.0029 29.4 1.2 18 3-21 103-120 (288)
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=9e-42 Score=294.27 Aligned_cols=128 Identities=37% Similarity=0.611 Sum_probs=95.5
Q ss_pred CCCCceECCChHHHHHHHHhhhcCCCCCCc-ceeEecCCCCCCCCCCCCCCCCCCCCcEEEEEeccccccCCCCcceeec
Q 016435 3 SLVGFRFHPTDEEIILLLTMKRRDPTGFSV-RTIKEIDLYSFEPRELPCHSDIQSEEEVWYFFCEPCYKNSESKRVHRRT 81 (389)
Q Consensus 3 LPpGfRF~PTDEELI~~YL~~Ki~G~plp~-~~I~evDVY~~ePweLP~~~~~~g~d~eWYFFs~r~rK~~~G~R~~R~t 81 (389)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||++|||+|++.. .+.+++||||+++.+++.++.|.+|++
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 899999999999999999999999999888 69999999999999999422 224789999999999999999999999
Q ss_pred cCceEEecCCcceeeeCCCceEEEEEEEEeeccccCCCCCCCcCeEEEEEEeC
Q 016435 82 KEGYWKKTGRGSNINRKYKTEVIGTKKFLSFSRDDAAAQKNTTEWVIHEIAVE 134 (389)
Q Consensus 82 ggG~WKatG~~K~I~~~~gg~vIG~KKtLvFy~gr~p~~g~KT~WvMhEYsL~ 134 (389)
++|+||++|+.++|.+. ++.+||+|++|+||.++.+ ++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~-~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSP-NGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTT-S-EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccc-cceeeeeEEEEEEEeccCC-CCCcCCeEEEEEEeC
Confidence 99999999999999996 4589999999999988777 889999999999984
No 2
>PHA00692 hypothetical protein
Probab=27.16 E-value=23 Score=28.08 Aligned_cols=9 Identities=44% Similarity=0.763 Sum_probs=7.4
Q ss_pred CCCCCceEC
Q 016435 2 DSLVGFRFH 10 (389)
Q Consensus 2 ~LPpGfRF~ 10 (389)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 579999995
No 3
>PF08483 IstB_IS21_ATP: IstB-like ATP binding N-terminal; InterPro: IPR013690 This bacterial domain is found to the N terminus of the IPR002611 from INTERPRO-like ATP binding domain in proteins which are putative transposase subunits [].
Probab=15.84 E-value=1.1e+02 Score=20.89 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=15.3
Q ss_pred chhhhHhHHHHhhhHHHHH
Q 016435 365 ETESFNEWVNMVFDYQILK 383 (389)
Q Consensus 365 ~~~~~~~~~~~~~~~~~~~ 383 (389)
..-||.||+.+..|-.+..
T Consensus 10 ~~LsFeERl~LLvdrE~~~ 28 (30)
T PF08483_consen 10 QELSFEERLGLLVDREWTW 28 (30)
T ss_pred hhcCHHHHHHHHHHHHHHh
Confidence 4568999999999877654
No 4
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=14.41 E-value=1.3e+02 Score=29.19 Aligned_cols=62 Identities=18% Similarity=0.243 Sum_probs=36.6
Q ss_pred CCCceECCChHHHHHHHHhhhcCCCCCCcceeEecCCCCCCCCCCCCCCCCCCCCcEEEEEe
Q 016435 4 LVGFRFHPTDEEIILLLTMKRRDPTGFSVRTIKEIDLYSFEPRELPCHSDIQSEEEVWYFFC 65 (389)
Q Consensus 4 PpGfRF~PTDEELI~~YL~~Ki~G~plp~~~I~evDVY~~ePweLP~~~~~~g~d~eWYFFs 65 (389)
--+|||.|+|.--+.-.-.-.....-+-+....+.+-|.-+=|+..+....+|+...||=+.
T Consensus 110 i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~~~~t~d 171 (216)
T KOG3238|consen 110 ITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSPNSYTYD 171 (216)
T ss_pred cccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCccccccc
Confidence 35899999998766643334444443322235666677777777754444445555665543
No 5
>COG5450 Transcription regulator of the Arc/MetJ class [Transcription]
Probab=13.61 E-value=76 Score=26.63 Aligned_cols=25 Identities=36% Similarity=0.356 Sum_probs=21.4
Q ss_pred hHHHHHhHHHhhcCCCCCCCCcccc
Q 016435 260 EAETRRLAELNRRGDGYDGRNDASV 284 (389)
Q Consensus 260 ~~~~~~~~~~~~~~~~~~~~~~~~~ 284 (389)
|+.++.|..++++++|+.|+||--.
T Consensus 52 e~~~r~l~~~~~~~~g~~~~~~~V~ 76 (84)
T COG5450 52 ERGTRILLLRALRAVGFTGDNDRVD 76 (84)
T ss_pred ccchhHHHhhhhhhccccCchHHHH
Confidence 7778888899999999999998543
No 6
>PLN02417 dihydrodipicolinate synthase
Probab=11.65 E-value=1.2e+02 Score=29.70 Aligned_cols=18 Identities=11% Similarity=0.041 Sum_probs=14.6
Q ss_pred CCCCceECCChHHHHHHHH
Q 016435 3 SLVGFRFHPTDEEIILLLT 21 (389)
Q Consensus 3 LPpGfRF~PTDEELI~~YL 21 (389)
+|| +.|.||+++|+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 566 568999999999774
No 7
>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=11.35 E-value=1.2e+02 Score=30.13 Aligned_cols=18 Identities=0% Similarity=-0.119 Sum_probs=14.8
Q ss_pred CCCCCceECCChHHHHHHH
Q 016435 2 DSLVGFRFHPTDEEIILLL 20 (389)
Q Consensus 2 ~LPpGfRF~PTDEELI~~Y 20 (389)
-+|| |.|.||+++|+.||
T Consensus 109 v~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 109 LGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred ECCC-cCCCCCHHHHHHHH
Confidence 4677 66899999999976
No 8
>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]
Probab=10.79 E-value=1.3e+02 Score=32.39 Aligned_cols=26 Identities=12% Similarity=0.227 Sum_probs=22.7
Q ss_pred CcchhhhHhHHHHhhhHHHHHHhhhc
Q 016435 363 NSETESFNEWVNMVFDYQILKEDIRS 388 (389)
Q Consensus 363 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 388 (389)
-+-...|+.|++|-+||++|-+|+|.
T Consensus 330 l~~ia~F~r~ad~s~d~nli~~alr~ 355 (448)
T KOG2590|consen 330 LRVIAKFKRVADLSSDINLILAALRN 355 (448)
T ss_pred hhhhhhhhhhhhcccCHHHHHHHHhh
Confidence 44567899999999999999999985
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=10.58 E-value=1.3e+02 Score=27.02 Aligned_cols=11 Identities=36% Similarity=0.582 Sum_probs=9.3
Q ss_pred CCChHHHHHHH
Q 016435 10 HPTDEEIILLL 20 (389)
Q Consensus 10 ~PTDEELI~~Y 20 (389)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999865
No 10
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=10.53 E-value=1.3e+02 Score=29.36 Aligned_cols=18 Identities=17% Similarity=-0.147 Sum_probs=13.7
Q ss_pred CCCCceECCChHHHHHHHH
Q 016435 3 SLVGFRFHPTDEEIILLLT 21 (389)
Q Consensus 3 LPpGfRF~PTDEELI~~YL 21 (389)
+||- .|.||++||+.||.
T Consensus 103 ~~P~-y~~~~~~~i~~~~~ 120 (288)
T cd00954 103 ITPF-YYKFSFEEIKDYYR 120 (288)
T ss_pred eCCC-CCCCCHHHHHHHHH
Confidence 4554 47899999999764
Done!