Query 037198
Match_columns 308
No_of_seqs 161 out of 972
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:42:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037198.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037198hhsearch_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 8E-42 1.7E-46 286.5 8.6 128 9-147 1-129 (129)
2 PHA00692 hypothetical protein 34.0 15 0.00033 27.7 0.3 11 7-17 35-45 (74)
3 PF10440 WIYLD: Ubiquitin-bind 25.6 58 0.0013 24.8 2.2 26 252-277 15-42 (65)
4 KOG0793 Protein tyrosine phosp 23.2 31 0.00067 37.6 0.4 24 280-306 851-875 (1004)
5 PF07960 CBP4: CBP4; InterPro 18.5 61 0.0013 27.9 1.1 18 15-32 29-49 (128)
6 smart00265 BH4 BH4 Bcl-2 homol 18.5 1E+02 0.0022 19.6 1.9 15 18-32 4-18 (27)
7 PF08938 HBS1_N: HBS1 N-termin 15.0 67 0.0015 24.8 0.5 16 288-304 45-60 (79)
8 PF01473 CW_binding_1: Putativ 14.7 1.1E+02 0.0025 17.1 1.3 8 72-79 7-14 (19)
9 cd00950 DHDPS Dihydrodipicolin 13.9 1.6E+02 0.0035 27.4 2.9 23 7-32 100-122 (284)
10 PF13822 ACC_epsilon: Acyl-CoA 13.3 97 0.0021 23.0 1.0 10 15-24 9-18 (62)
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=8e-42 Score=286.45 Aligned_cols=128 Identities=28% Similarity=0.518 Sum_probs=91.8
Q ss_pred CCCCceeCCChHHHHHHHHHHhHhcCCCCCCCCCCcccccCCCCCCCCcchhhhhcCCCcccCCceEEEEeeccccCCCC
Q 037198 9 FYPVLRFYPTEQELLEFYLLHKITQNHNLYQASDDIPVKDCDLYSPHEPNLIWDLYGGDQLMAGQALYFFTQLKKASPKG 88 (308)
Q Consensus 9 LPpGfRF~PTDeELI~~YL~~Ki~~g~~lp~~~~~~~I~evDlY~~~ePwdLp~~~g~~~~~~~~eWYFFs~r~rk~~~G 88 (308)
|||||||+|||+|||.+||++|+. |.+++ ...+|+++||| .+|||+|+..+ ..++.+||||+++++++++|
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~-g~~~~---~~~~i~~~Diy-~~~P~~L~~~~----~~~~~~~yFF~~~~~~~~~~ 71 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKIL-GEPLP---CEDVIHDVDIY-SAHPWELPAKF----KGGDEEWYFFSPRKKKYPNG 71 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHT-T-HHC---S-CHSEE--GG-GS-GGGCHHHS----SS-SSEEEEEEE--------
T ss_pred CCCceEecCChHHHHHHHHHHHhc-CCCCC---cccceeecccC-ccChHHhhhhc----cCCCceEEEEEecccccCCc
Confidence 899999999999999999999999 66664 34689999999 59999999532 23677999999999999999
Q ss_pred CccceeeccceeeecCCCeEEEecCCCCeEEEEEEEEeee-cCCCCCCCcCeEEEEEEeC
Q 037198 89 SRFNIKIGFDAWQGEDRAKLVLAVGSEDQILGFKKRFRYE-SRENLEQNGRWIMHEFTIN 147 (308)
Q Consensus 89 ~R~~Rat~~G~WK~tG~~k~I~~~~~~g~vVG~KKtLvF~-~r~p~g~kT~WvMhEY~L~ 147 (308)
.|.+|++++|+||++|++++|.+. ++.+||+|++|+|+ ++.+++.+|+|+||||+|+
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 GRPNRVTGGGYWKSTGKEKPIKDP--GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp --S-EEETTEEEEEECEEEEEEE---TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccccccccceEEeecccccccccc--cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999999999999986 38899999999997 4556789999999999984
No 2
>PHA00692 hypothetical protein
Probab=33.99 E-value=15 Score=27.66 Aligned_cols=11 Identities=27% Similarity=0.504 Sum_probs=8.7
Q ss_pred CCCCCCceeCC
Q 037198 7 LRFYPVLRFYP 17 (308)
Q Consensus 7 ~~LPpGfRF~P 17 (308)
...||||||--
T Consensus 35 veyppgfrfgg 45 (74)
T PHA00692 35 VEYPPGFRFGG 45 (74)
T ss_pred EecCCCccccc
Confidence 46899999953
No 3
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=25.55 E-value=58 Score=24.84 Aligned_cols=26 Identities=15% Similarity=0.305 Sum_probs=22.0
Q ss_pred hhcc--cccCchhHHHHHHHHhhhhcCC
Q 037198 252 VESE--VGIDSLPNKLVFNILVFYFKKN 277 (308)
Q Consensus 252 ~~~~--~~~~~~~~~~~~~~~~~~~~~~ 277 (308)
+..+ +||+...++-||++|-++.+++
T Consensus 15 ~dam~~lG~~~~~v~~vl~~LL~lY~~n 42 (65)
T PF10440_consen 15 LDAMRQLGFSKKQVRPVLKNLLKLYDGN 42 (65)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHcCC
Confidence 4444 9999999999999999977766
No 4
>KOG0793 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=23.22 E-value=31 Score=37.60 Aligned_cols=24 Identities=42% Similarity=0.755 Sum_probs=19.3
Q ss_pred CCcccee-eccccccchhhhhhhhhhee
Q 037198 280 GEETEVY-LREESIVNEALIHHYCEIFL 306 (308)
Q Consensus 280 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 306 (308)
-||+|+| .-||-+++|+|| ||=||
T Consensus 851 deGselyhiyEV~LVSEHIW---ceDfL 875 (1004)
T KOG0793|consen 851 DEGSELYHIYEVNLVSEHIW---CEDFL 875 (1004)
T ss_pred CCCcceeeeEEeeeehhhhh---hhhHH
Confidence 4679998 579999999999 66555
No 5
>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=18.51 E-value=61 Score=27.92 Aligned_cols=18 Identities=39% Similarity=0.552 Sum_probs=12.8
Q ss_pred eCCChHHHHHHH---HHHhHh
Q 037198 15 FYPTEQELLEFY---LLHKIT 32 (308)
Q Consensus 15 F~PTDeELI~~Y---L~~Ki~ 32 (308)
=.||||||+..| |+++..
T Consensus 29 ~tPTeEeL~~r~sPELrkr~~ 49 (128)
T PF07960_consen 29 TTPTEEELFKRYSPELRKRYL 49 (128)
T ss_pred cCCCHHHHHHhcCHHHHHHHH
Confidence 369999999875 444443
No 6
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=18.50 E-value=1e+02 Score=19.64 Aligned_cols=15 Identities=27% Similarity=0.423 Sum_probs=13.5
Q ss_pred ChHHHHHHHHHHhHh
Q 037198 18 TEQELLEFYLLHKIT 32 (308)
Q Consensus 18 TDeELI~~YL~~Ki~ 32 (308)
+-.|||.+|+.-|+.
T Consensus 4 ~nRelV~~yv~yKLs 18 (27)
T smart00265 4 DNRELVVDYVTYKLS 18 (27)
T ss_pred chHHHHHHHHHHHHh
Confidence 458999999999998
No 7
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=15.03 E-value=67 Score=24.77 Aligned_cols=16 Identities=50% Similarity=0.700 Sum_probs=9.7
Q ss_pred ccccccchhhhhhhhhh
Q 037198 288 REESIVNEALIHHYCEI 304 (308)
Q Consensus 288 ~~~~~~~~~~~~~~~~~ 304 (308)
++..|. +++|+||+.+
T Consensus 45 ~e~~i~-eal~~~~fDv 60 (79)
T PF08938_consen 45 PEEQIK-EALWHYYFDV 60 (79)
T ss_dssp -CCHHH-HHHHHTTT-C
T ss_pred CHHHHH-HHHHHHcCCH
Confidence 344444 4899999875
No 8
>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=14.69 E-value=1.1e+02 Score=17.05 Aligned_cols=8 Identities=25% Similarity=0.762 Sum_probs=6.6
Q ss_pred CceEEEEe
Q 037198 72 GQALYFFT 79 (308)
Q Consensus 72 ~~eWYFFs 79 (308)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 58899994
No 9
>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=13.87 E-value=1.6e+02 Score=27.38 Aligned_cols=23 Identities=22% Similarity=0.392 Sum_probs=16.9
Q ss_pred CCCCCCceeCCChHHHHHHHHHHhHh
Q 037198 7 LRFYPVLRFYPTEQELLEFYLLHKIT 32 (308)
Q Consensus 7 ~~LPpGfRF~PTDeELI~~YL~~Ki~ 32 (308)
+-+||.+ |.|+++||+.|| ++|.
T Consensus 100 ~~~~P~~-~~~~~~~l~~~~--~~ia 122 (284)
T cd00950 100 LVVTPYY-NKPSQEGLYAHF--KAIA 122 (284)
T ss_pred EEccccc-CCCCHHHHHHHH--HHHH
Confidence 3456654 789999999977 5555
No 10
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=13.30 E-value=97 Score=22.99 Aligned_cols=10 Identities=40% Similarity=0.478 Sum_probs=8.2
Q ss_pred eCCChHHHHH
Q 037198 15 FYPTEQELLE 24 (308)
Q Consensus 15 F~PTDeELI~ 24 (308)
=+||||||-.
T Consensus 9 GnPt~eElAA 18 (62)
T PF13822_consen 9 GNPTDEELAA 18 (62)
T ss_pred CCCCHHHHHH
Confidence 3799999975
Done!