Query 020354
Match_columns 327
No_of_seqs 195 out of 931
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 09:04:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020354.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020354hhsearch_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 4E-43 8.6E-48 296.4 7.7 127 7-136 1-129 (129)
2 PHA00692 hypothetical protein 41.8 9 0.0002 29.4 0.1 12 4-15 34-45 (74)
3 KOG3238 Chloride ion current i 20.1 1.3E+02 0.0028 28.5 3.7 61 9-70 111-171 (216)
4 smart00265 BH4 BH4 Bcl-2 homol 13.9 1.5E+02 0.0032 19.3 1.8 17 16-32 4-20 (27)
5 PF07960 CBP4: CBP4; InterPro 13.3 99 0.0021 27.1 1.1 11 14-24 30-40 (128)
6 PF04700 Baculo_gp41: Structur 12.9 1.8E+02 0.0039 27.0 2.7 17 16-32 6-24 (186)
7 PLN02417 dihydrodipicolinate s 12.4 1.3E+02 0.0028 28.7 1.8 19 7-26 103-121 (280)
8 PF01473 CW_binding_1: Putativ 12.1 1.5E+02 0.0032 16.9 1.3 7 64-70 8-14 (19)
9 PF09174 Maf1: Maf1 regulator; 12.1 59 0.0013 29.4 -0.6 36 39-74 137-173 (179)
10 cd00954 NAL N-Acetylneuraminic 11.5 1.6E+02 0.0035 28.0 2.1 19 7-26 103-121 (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=4e-43 Score=296.37 Aligned_cols=127 Identities=54% Similarity=1.101 Sum_probs=96.5
Q ss_pred CCCCcEECCChHHHHHHHHHHHhccCCCCC-CceeeccCCCCCCcchhhhhhcCCCCCceEEEEecCCCCCCCCCccccc
Q 020354 7 VPPGFRFHPTDEELVDYYLRKKVASKRIDL-DVIKDVDLYKIEPWDLQELCKIGSEEQNEWYFFSHKDKKYPTGTRTNRA 85 (327)
Q Consensus 7 LPpGfRF~PTDEELI~~YLr~Kv~g~pl~~-~~I~dvDVY~~ePwdLp~~~~~g~~~~~~WYFFs~~~kk~~~G~R~nRa 85 (327)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||++|||+|+.... ..+.+||||+++++++++|.|++|+
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~---~~~~~~yFF~~~~~~~~~~~r~~R~ 77 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFK---GGDEEWYFFSPRKKKYPNGGRPNRV 77 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSS---S-SSEEEEEEE----------S-EE
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhcc---CCCceEEEEEecccccCCccccccc
Confidence 899999999999999999999999999887 799999999999999995222 2345999999999999999999999
Q ss_pred ccCceeeecCCCeeEec-CCeeEEeEEEEEEeeccCCCCCCcCeEEEEEEeC
Q 020354 86 TKAGFWKATGRDKAIYS-RHSLIGMRKTLVFYKGRAPNGQKSDWIMHEYRLE 136 (327)
Q Consensus 86 tggG~WK~tG~~k~I~~-~g~lIG~KKtLvFy~gr~p~g~KT~WvMhEY~L~ 136 (327)
+++|+||++|+.++|.. ++.+||+|++|+||.++.+++.||+|+||||+|+
T Consensus 78 ~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 78 TGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp ETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred ccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999999999999998 8999999999999998888899999999999985
No 2
>PHA00692 hypothetical protein
Probab=41.83 E-value=9 Score=29.44 Aligned_cols=12 Identities=58% Similarity=1.187 Sum_probs=9.3
Q ss_pred CCCCCCCcEECC
Q 020354 4 FSHVPPGFRFHP 15 (327)
Q Consensus 4 ~~~LPpGfRF~P 15 (327)
+...||||||--
T Consensus 34 fveyppgfrfgg 45 (74)
T PHA00692 34 FVEYPPGFRFGG 45 (74)
T ss_pred eEecCCCccccc
Confidence 457899999953
No 3
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=20.09 E-value=1.3e+02 Score=28.45 Aligned_cols=61 Identities=21% Similarity=0.413 Sum_probs=36.5
Q ss_pred CCcEECCChHHHHHHHHHHHhccCCCCCCceeeccCCCCCCcchhhhhhcCCCCCceEEEEe
Q 020354 9 PGFRFHPTDEELVDYYLRKKVASKRIDLDVIKDVDLYKIEPWDLQELCKIGSEEQNEWYFFS 70 (327)
Q Consensus 9 pGfRF~PTDEELI~~YLr~Kv~g~pl~~~~I~dvDVY~~ePwdLp~~~~~g~~~~~~WYFFs 70 (327)
-+|||+|+|.--+...-.....+..+-+....+.+-|.-+=|+.-.- ..|.++...||=+.
T Consensus 111 ~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dgee~~mea~-d~~~gDs~~~~t~d 171 (216)
T KOG3238|consen 111 TEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGEEYDMEAH-DAGQGDSPNSYTYD 171 (216)
T ss_pred ccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccchhhhhhh-hccCCCCccccccc
Confidence 48999999998777633333334433333466777787777777543 44444444555443
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=13.88 E-value=1.5e+02 Score=19.32 Aligned_cols=17 Identities=29% Similarity=0.438 Sum_probs=13.9
Q ss_pred ChHHHHHHHHHHHhccC
Q 020354 16 TDEELVDYYLRKKVASK 32 (327)
Q Consensus 16 TDEELI~~YLr~Kv~g~ 32 (327)
+-.|||.+|+.-|+.-.
T Consensus 4 ~nRelV~~yv~yKLsQr 20 (27)
T smart00265 4 DNRELVVDYVTYKLSQN 20 (27)
T ss_pred chHHHHHHHHHHHHhhc
Confidence 56899999999998543
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=13.34 E-value=99 Score=27.07 Aligned_cols=11 Identities=55% Similarity=0.918 Sum_probs=9.4
Q ss_pred CCChHHHHHHH
Q 020354 14 HPTDEELVDYY 24 (327)
Q Consensus 14 ~PTDEELI~~Y 24 (327)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 6
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=12.91 E-value=1.8e+02 Score=27.01 Aligned_cols=17 Identities=47% Similarity=0.868 Sum_probs=10.9
Q ss_pred ChHHHHHHHH--HHHhccC
Q 020354 16 TDEELVDYYL--RKKVASK 32 (327)
Q Consensus 16 TDEELI~~YL--r~Kv~g~ 32 (327)
+|||||.||- .+|..|.
T Consensus 6 sDe~Li~yY~~L~K~~g~~ 24 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGS 24 (186)
T ss_pred cHHHHHHHHHHHHHHhCCC
Confidence 7888888884 3444443
No 7
>PLN02417 dihydrodipicolinate synthase
Probab=12.41 E-value=1.3e+02 Score=28.66 Aligned_cols=19 Identities=16% Similarity=0.375 Sum_probs=15.0
Q ss_pred CCCCcEECCChHHHHHHHHH
Q 020354 7 VPPGFRFHPTDEELVDYYLR 26 (327)
Q Consensus 7 LPpGfRF~PTDEELI~~YLr 26 (327)
+|| +.|.||++||+.||-.
T Consensus 103 ~~P-~y~~~~~~~i~~~f~~ 121 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFET 121 (280)
T ss_pred cCC-ccCCCCHHHHHHHHHH
Confidence 566 5589999999999753
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=12.10 E-value=1.5e+02 Score=16.90 Aligned_cols=7 Identities=43% Similarity=1.706 Sum_probs=5.8
Q ss_pred ceEEEEe
Q 020354 64 NEWYFFS 70 (327)
Q Consensus 64 ~~WYFFs 70 (327)
+.||||.
T Consensus 8 ~~wYy~~ 14 (19)
T PF01473_consen 8 GNWYYFD 14 (19)
T ss_dssp TEEEEET
T ss_pred CEEEEeC
Confidence 5899994
No 9
>PF09174 Maf1: Maf1 regulator; InterPro: IPR015257 Maf1 is a negative regulator of RNA polymerase III [, ]. It targets the initiation factor TFIIIB []. ; PDB: 3NR5_A.
Probab=12.05 E-value=59 Score=29.42 Aligned_cols=36 Identities=25% Similarity=0.420 Sum_probs=15.0
Q ss_pred eeeccCCCCCCcchhhhh-hcCCCCCceEEEEecCCC
Q 020354 39 IKDVDLYKIEPWDLQELC-KIGSEEQNEWYFFSHKDK 74 (327)
Q Consensus 39 I~dvDVY~~ePwdLp~~~-~~g~~~~~~WYFFs~~~k 74 (327)
+.+||||.+.|-.-.+.+ ..|.--.-.||||.++.|
T Consensus 137 l~~C~iYsy~pd~~~dPf~e~g~lws~~yff~nkk~K 173 (179)
T PF09174_consen 137 LKDCDIYSYNPDSDSDPFAEDGCLWSFNYFFYNKKLK 173 (179)
T ss_dssp GGG-EEEEE---GGG-TT-S---SEEEEEEEEETTTT
T ss_pred ccCceEEEEccCCCCCccccccchheeeeeEEecCcc
Confidence 568999999984322222 223222224566665543
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=11.47 E-value=1.6e+02 Score=27.99 Aligned_cols=19 Identities=32% Similarity=0.639 Sum_probs=14.5
Q ss_pred CCCCcEECCChHHHHHHHHH
Q 020354 7 VPPGFRFHPTDEELVDYYLR 26 (327)
Q Consensus 7 LPpGfRF~PTDEELI~~YLr 26 (327)
+||-| |.||++||+.||..
T Consensus 103 ~~P~y-~~~~~~~i~~~~~~ 121 (288)
T cd00954 103 ITPFY-YKFSFEEIKDYYRE 121 (288)
T ss_pred eCCCC-CCCCHHHHHHHHHH
Confidence 45544 78999999998754
Done!