Query 021772
Match_columns 307
No_of_seqs 169 out of 896
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 05:33:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021772hhsearch_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 8.8E-43 1.9E-47 292.1 6.2 127 3-133 1-129 (129)
2 PHA00692 hypothetical protein 24.1 29 0.00062 26.1 0.2 9 2-10 36-44 (74)
3 PF07960 CBP4: CBP4; InterPro 16.4 72 0.0016 27.4 1.1 17 9-25 29-49 (128)
4 PF08061 P68HR: P68HR (NUC004) 12.7 82 0.0018 21.0 0.4 14 261-274 10-23 (33)
5 smart00707 RPEL Repeat in Dros 12.7 1.4E+02 0.0029 18.8 1.3 13 6-18 6-18 (26)
6 COG3100 Uncharacterized protei 12.0 1.5E+02 0.0032 24.4 1.7 15 140-154 8-22 (103)
7 cd00950 DHDPS Dihydrodipicolin 11.3 1.8E+02 0.004 27.0 2.4 27 3-30 102-128 (284)
8 PF13822 ACC_epsilon: Acyl-CoA 11.0 1.3E+02 0.0027 22.3 1.0 9 10-18 10-18 (62)
9 KOG3238 Chloride ion current i 10.8 1.9E+02 0.0042 26.8 2.2 60 4-63 110-170 (216)
10 PF01473 CW_binding_1: Putativ 10.3 1.9E+02 0.0041 16.1 1.3 8 57-64 7-14 (19)
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=8.8e-43 Score=292.14 Aligned_cols=127 Identities=43% Similarity=0.741 Sum_probs=95.8
Q ss_pred CCCCceecCCHHHHHH-HhHHhhCCCCCCc-ceeeeccCCCCCCCCCCCcCccCCCCceEEEeecccccccCCccccccC
Q 021772 3 SLVGFRFHPTDEEIIL-LLTLKRFDPGFSV-RTIKEIDLYSFEPWELPWHSEIQSEEEVWYFFCEPYYKYAKSKRANRRT 80 (307)
Q Consensus 3 LPpGfRF~PTDeELV~-YL~~Ki~g~plp~-~~I~evDvY~~ePweLp~~~~~~~~e~~wYFFs~r~rk~~~G~R~~R~t 80 (307)
|||||||+|||+|||. ||++||.|.+++. .+|+++|||++|||+||.... ..+.+||||+++++++.++.|.+|++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~--~~~~~~yFF~~~~~~~~~~~r~~R~~ 78 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFK--GGDEEWYFFSPRKKKYPNGGRPNRVT 78 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSS--S-SSEEEEEEE----------S-EEE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhcc--CCCceEEEEEecccccCCcccccccc
Confidence 8999999999999999 9999999999988 899999999999999994222 23779999999999999999999999
Q ss_pred CCceEEecCCCceEEeCCCCEEEeEEEEeeeecccCCCCCCccCeeEeEEeec
Q 021772 81 KEGYWKKTGNGSKIKRKYSTEVIGTKKILSFLRDDTAAKKAKTEWVIHEIAVE 133 (307)
Q Consensus 81 g~G~Wk~tG~~k~I~~~~~g~vVG~KktL~Fy~g~r~~~g~kT~WvMhEY~l~ 133 (307)
++|+||++|+.+.|.+. ++.+||+|++|+||.+ +.+++.+|+|+||||+|.
T Consensus 79 ~~G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~-~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 79 GGGYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSG-KSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp TTEEEEEECEEEEEEE--TTCEEEEEEEEEEEES-STTS-EEEEEEEEEEEE-
T ss_pred cceEEeecccccccccc-cceeeeeEEEEEEEec-cCCCCCcCCeEEEEEEeC
Confidence 99999999999999985 6899999999999998 788899999999999984
No 2
>PHA00692 hypothetical protein
Probab=24.11 E-value=29 Score=26.15 Aligned_cols=9 Identities=44% Similarity=0.763 Sum_probs=7.2
Q ss_pred CCCCCceec
Q 021772 2 DSLVGFRFH 10 (307)
Q Consensus 2 ~LPpGfRF~ 10 (307)
..||||||-
T Consensus 36 eyppgfrfg 44 (74)
T PHA00692 36 EYPPGFRFG 44 (74)
T ss_pred ecCCCcccc
Confidence 478999985
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=16.37 E-value=72 Score=27.44 Aligned_cols=17 Identities=29% Similarity=0.467 Sum_probs=12.0
Q ss_pred ecCCHHHHHH-H---hHHhhC
Q 021772 9 FHPTDEEIIL-L---LTLKRF 25 (307)
Q Consensus 9 F~PTDeELV~-Y---L~~Ki~ 25 (307)
-.||||||+. | |+++..
T Consensus 29 ~tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 29 TTPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred cCCCHHHHHHhcCHHHHHHHH
Confidence 3799999998 5 444443
No 4
>PF08061 P68HR: P68HR (NUC004) repeat; InterPro: IPR012587 This short region is found in two copies in p68-like RNA helicases [].; GO: 0003712 transcription cofactor activity, 0003724 RNA helicase activity, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0005634 nucleus
Probab=12.72 E-value=82 Score=20.96 Aligned_cols=14 Identities=43% Similarity=0.617 Sum_probs=11.2
Q ss_pred CCCchhcccccccc
Q 021772 261 QFNSRRDFQNEYSS 274 (307)
Q Consensus 261 ~~~~~~~~~~~~~~ 274 (307)
-+|-++++++||+|
T Consensus 10 t~~~~~~Yq~GY~s 23 (33)
T PF08061_consen 10 TGRDRENYQNGYSS 23 (33)
T ss_pred ccCcccchhcccch
Confidence 45677889999996
No 5
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=12.65 E-value=1.4e+02 Score=18.83 Aligned_cols=13 Identities=31% Similarity=0.335 Sum_probs=11.0
Q ss_pred CceecCCHHHHHH
Q 021772 6 GFRFHPTDEEIIL 18 (307)
Q Consensus 6 GfRF~PTDeELV~ 18 (307)
...++|+-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3568999999997
No 6
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=12.02 E-value=1.5e+02 Score=24.41 Aligned_cols=15 Identities=13% Similarity=0.408 Sum_probs=11.8
Q ss_pred CCeEEEEEEEeCCCC
Q 021772 140 KDFVVCRLERKRDKK 154 (307)
Q Consensus 140 ~~~VLCRIykK~~~~ 154 (307)
.--.||-|||++++.
T Consensus 8 ~~~mlCaIYkS~kk~ 22 (103)
T COG3100 8 SKSMLCAIYKSPKKD 22 (103)
T ss_pred ceeeeeeeeecCcCC
Confidence 345899999998764
No 7
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=11.35 E-value=1.8e+02 Score=27.00 Aligned_cols=27 Identities=7% Similarity=0.038 Sum_probs=20.0
Q ss_pred CCCCceecCCHHHHHHHhHHhhCCCCCC
Q 021772 3 SLVGFRFHPTDEEIILLLTLKRFDPGFS 30 (307)
Q Consensus 3 LPpGfRF~PTDeELV~YL~~Ki~g~plp 30 (307)
+||.| |.|+++||+.|.+.-+...++|
T Consensus 102 ~~P~~-~~~~~~~l~~~~~~ia~~~~~p 128 (284)
T cd00950 102 VTPYY-NKPSQEGLYAHFKAIAEATDLP 128 (284)
T ss_pred ccccc-CCCCHHHHHHHHHHHHhcCCCC
Confidence 56644 8899999999877776655555
No 8
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=11.04 E-value=1.3e+02 Score=22.35 Aligned_cols=9 Identities=56% Similarity=0.888 Sum_probs=7.7
Q ss_pred cCCHHHHHH
Q 021772 10 HPTDEEIIL 18 (307)
Q Consensus 10 ~PTDeELV~ 18 (307)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999866
No 9
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=10.81 E-value=1.9e+02 Score=26.79 Aligned_cols=60 Identities=20% Similarity=0.272 Sum_probs=32.5
Q ss_pred CCCceecCCHHHHHH-HhHHhhCCCCCCcceeeeccCCCCCCCCCCCcCccCCCCceEEEe
Q 021772 4 LVGFRFHPTDEEIIL-LLTLKRFDPGFSVRTIKEIDLYSFEPWELPWHSEIQSEEEVWYFF 63 (307)
Q Consensus 4 PpGfRF~PTDeELV~-YL~~Ki~g~plp~~~I~evDvY~~ePweLp~~~~~~~~e~~wYFF 63 (307)
--+|||+|+|.--+. --.-......+-.....+.+-|.-+=|+.-.....+++...||=+
T Consensus 110 i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~d~~~gDs~~~~t~ 170 (216)
T KOG3238|consen 110 ITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAHDAGQGDSPNSYTY 170 (216)
T ss_pred cccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhhhccCCCCcccccc
Confidence 347999999988777 333333333332222455566666666664443333334444433
No 10
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=10.29 E-value=1.9e+02 Score=16.10 Aligned_cols=8 Identities=38% Similarity=1.198 Sum_probs=6.5
Q ss_pred CceEEEee
Q 021772 57 EEVWYFFC 64 (307)
Q Consensus 57 e~~wYFFs 64 (307)
+..||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899994
Done!