Query 038703
Match_columns 199
No_of_seqs 118 out of 959
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 02:29:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038703.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038703hhsearch_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 5.6E-45 1.2E-49 278.9 7.9 125 18-146 1-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 51.5 25 0.00055 19.5 2.9 22 26-47 3-24 (27)
3 PHA00692 hypothetical protein 43.2 10 0.00022 25.1 0.5 10 16-25 35-44 (74)
4 PF07960 CBP4: CBP4; InterPro 37.0 18 0.0004 27.6 1.2 11 25-35 30-40 (128)
5 COG2326 Uncharacterized conser 35.7 35 0.00075 29.3 2.7 45 4-48 85-133 (270)
6 PF02180 BH4: Bcl-2 homology r 34.6 46 0.00099 18.5 2.2 21 27-47 4-24 (27)
7 cd00952 CHBPH_aldolase Trans-o 29.9 25 0.00055 30.5 1.0 32 10-43 102-133 (309)
8 PF13822 ACC_epsilon: Acyl-CoA 29.8 28 0.00061 23.0 1.0 9 25-33 10-18 (62)
9 smart00707 RPEL Repeat in Dros 29.4 39 0.00084 18.6 1.3 13 21-33 6-18 (26)
10 PLN02417 dihydrodipicolinate s 29.4 31 0.00067 29.4 1.4 23 13-36 98-120 (280)
11 PF08338 DUF1731: Domain of un 27.0 46 0.001 20.8 1.6 17 19-35 30-47 (48)
12 PF01473 CW_binding_1: Putativ 26.9 47 0.001 16.2 1.3 8 74-81 7-14 (19)
13 cd00954 NAL N-Acetylneuraminic 26.8 34 0.00074 29.2 1.3 28 14-43 99-126 (288)
14 TIGR02313 HpaI-NOT-DapA 2,4-di 26.1 39 0.00085 29.0 1.5 31 11-43 95-125 (294)
15 KOG3238 Chloride ion current i 24.9 85 0.0018 25.9 3.1 50 15-65 106-155 (216)
16 TIGR00674 dapA dihydrodipicoli 22.6 51 0.0011 28.0 1.6 34 11-46 93-126 (285)
17 PF04700 Baculo_gp41: Structur 21.7 91 0.002 25.3 2.7 21 27-47 6-28 (186)
18 cd00950 DHDPS Dihydrodipicolin 21.6 86 0.0019 26.4 2.8 34 11-46 95-128 (284)
19 cd00490 Met_repressor_MetJ Met 21.5 1.2E+02 0.0026 21.7 3.0 37 25-66 50-86 (103)
20 PF01340 MetJ: Met Apo-repress 21.1 1.3E+02 0.0028 21.6 3.1 37 25-66 50-86 (104)
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=5.6e-45 Score=278.94 Aligned_cols=125 Identities=45% Similarity=0.910 Sum_probs=96.7
Q ss_pred CCCcceECCChHHHHHHHHHHHHhCCCCCC-CceeecccCCCCCCCCCCcccccCCCCCeEEEEeeecC--CCCCCCCcc
Q 038703 18 LPLGYRFSPNGQEIIVQYLTKKILNQRLPS-NIIKDIDLYAYDHPRQLPIGEFKNCKPDEGYFFTQLEN--RDGKGQPKR 94 (199)
Q Consensus 18 lppG~rF~PTDeELv~~YL~~ki~g~~l~~-~~I~~~Dvy~~~~P~~Lp~~~~~~~~~~~wyFF~~~~~--~~g~~r~~R 94 (199)
|||||||+|||+|||.+||++|+.|.+++. .+|+++|||+++ ||+|+ .....++++||||+++++ .+| .|.+|
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~-P~~L~--~~~~~~~~~~yFF~~~~~~~~~~-~r~~R 76 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAH-PWELP--AKFKGGDEEWYFFSPRKKKYPNG-GRPNR 76 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS--GGGCH--HHSSS-SSEEEEEEE-----------S-E
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccC-hHHhh--hhccCCCceEEEEEecccccCCc-ccccc
Confidence 899999999999999999999999999887 799999999999 99999 233335689999999987 566 88999
Q ss_pred cCCCceeeecCCceEEee-CCeEEEEEEEEEeeeCCCCCCCccCeEEEEEEeC
Q 038703 95 TTKSGYWKDTGKVEQIIW-NNSIVGFKKILVFYEGKPPTGTRSRWVMHEFRVN 146 (199)
Q Consensus 95 ~~~~G~Wk~~g~~k~I~~-~g~~iG~kk~l~fy~~~~~~g~kT~W~M~EY~l~ 146 (199)
++++|+||.+|+.++|.. ++.+||+|++|+||.++.+.+.+|+|+||||+|.
T Consensus 77 ~~~~G~Wk~~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 77 VTGGGYWKSTGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EETTEEEEEECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred cccceEEeecccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999999996 9999999999999998888889999999999983
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=51.46 E-value=25 Score=19.49 Aligned_cols=22 Identities=23% Similarity=0.397 Sum_probs=17.4
Q ss_pred CChHHHHHHHHHHHHhCCCCCC
Q 038703 26 PNGQEIIVQYLTKKILNQRLPS 47 (199)
Q Consensus 26 PTDeELv~~YL~~ki~g~~l~~ 47 (199)
.+-.|||.+|+.-|+.-...++
T Consensus 3 ~~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 3 LDNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred cchHHHHHHHHHHHHhhcCCCC
Confidence 3568999999999998766554
No 3
>PHA00692 hypothetical protein
Probab=43.18 E-value=10 Score=25.08 Aligned_cols=10 Identities=40% Similarity=1.062 Sum_probs=8.2
Q ss_pred CCCCCcceEC
Q 038703 16 FDLPLGYRFS 25 (199)
Q Consensus 16 ~~lppG~rF~ 25 (199)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4579999995
No 4
>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=37.03 E-value=18 Score=27.61 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=9.5
Q ss_pred CCChHHHHHHH
Q 038703 25 SPNGQEIIVQY 35 (199)
Q Consensus 25 ~PTDeELv~~Y 35 (199)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999875
No 5
>COG2326 Uncharacterized conserved protein [Function unknown]
Probab=35.73 E-value=35 Score=29.33 Aligned_cols=45 Identities=22% Similarity=0.240 Sum_probs=33.3
Q ss_pred CCcccccCCCCCCCCCCcceEC----CChHHHHHHHHHHHHhCCCCCCC
Q 038703 4 QGVFGSINQEEEFDLPLGYRFS----PNGQEIIVQYLTKKILNQRLPSN 48 (199)
Q Consensus 4 ~~~~~~~~~~~~~~lppG~rF~----PTDeELv~~YL~~ki~g~~l~~~ 48 (199)
+|+.|-|..=.+.--|-|+|-. |||+|+-..||.+.+...|--.+
T Consensus 85 AGKgG~Ikri~~~lNPR~~rvval~aPt~~E~~qwY~qRy~~~lPa~Ge 133 (270)
T COG2326 85 AGKGGAIKRITEALNPRGARVVALPAPTDRERGQWYFQRYVAHLPAAGE 133 (270)
T ss_pred cCCCchhHHHhhhcCCceeEEeecCCCChHhhccHHHHHHHHhCCCCCe
Confidence 4555555544455668898843 99999999999999988765544
No 6
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=34.55 E-value=46 Score=18.48 Aligned_cols=21 Identities=14% Similarity=0.360 Sum_probs=16.3
Q ss_pred ChHHHHHHHHHHHHhCCCCCC
Q 038703 27 NGQEIIVQYLTKKILNQRLPS 47 (199)
Q Consensus 27 TDeELv~~YL~~ki~g~~l~~ 47 (199)
+-.|||.+|+.-|+.-..+++
T Consensus 4 ~nR~lV~~yi~yKLsQrgy~w 24 (27)
T PF02180_consen 4 DNRELVEDYISYKLSQRGYVW 24 (27)
T ss_dssp HHHHHHHHHHHHHHHHTTSTS
T ss_pred cHHHHHHHHHHHHhhhcCCCC
Confidence 357999999999997665554
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=29.91 E-value=25 Score=30.45 Aligned_cols=32 Identities=3% Similarity=-0.080 Sum_probs=21.5
Q ss_pred cCCCCCCCCCCcceECCChHHHHHHHHHHHHhCC
Q 038703 10 INQEEEFDLPLGYRFSPNGQEIIVQYLTKKILNQ 43 (199)
Q Consensus 10 ~~~~~~~~lppG~rF~PTDeELv~~YL~~ki~g~ 43 (199)
+.-.+.+-+|| |.|.||++||+.|| +.-+...
T Consensus 102 ~Gad~vlv~~P-~y~~~~~~~l~~yf-~~va~a~ 133 (309)
T cd00952 102 LGADGTMLGRP-MWLPLDVDTAVQFY-RDVAEAV 133 (309)
T ss_pred hCCCEEEECCC-cCCCCCHHHHHHHH-HHHHHhC
Confidence 34445667788 66899999999865 4444433
No 8
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=29.81 E-value=28 Score=22.97 Aligned_cols=9 Identities=22% Similarity=0.612 Sum_probs=7.7
Q ss_pred CCChHHHHH
Q 038703 25 SPNGQEIIV 33 (199)
Q Consensus 25 ~PTDeELv~ 33 (199)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999865
No 9
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=29.41 E-value=39 Score=18.57 Aligned_cols=13 Identities=15% Similarity=0.169 Sum_probs=10.9
Q ss_pred cceECCChHHHHH
Q 038703 21 GYRFSPNGQEIIV 33 (199)
Q Consensus 21 G~rF~PTDeELv~ 33 (199)
...++||-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 4568999999997
No 10
>PLN02417 dihydrodipicolinate synthase
Probab=29.35 E-value=31 Score=29.43 Aligned_cols=23 Identities=9% Similarity=0.187 Sum_probs=17.1
Q ss_pred CCCCCCCCcceECCChHHHHHHHH
Q 038703 13 EEEFDLPLGYRFSPNGQEIIVQYL 36 (199)
Q Consensus 13 ~~~~~lppG~rF~PTDeELv~~YL 36 (199)
.+.+-+|| |.|.||++||+.||-
T Consensus 98 dav~~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 98 HAALHINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred CEEEEcCC-ccCCCCHHHHHHHHH
Confidence 34556677 558999999999763
No 11
>PF08338 DUF1731: Domain of unknown function (DUF1731); InterPro: IPR013549 This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (IPR001509 from INTERPRO) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. ; PDB: 3OH8_A.
Probab=27.00 E-value=46 Score=20.75 Aligned_cols=17 Identities=24% Similarity=0.554 Sum_probs=9.9
Q ss_pred CCcceEC-CChHHHHHHH
Q 038703 19 PLGYRFS-PNGQEIIVQY 35 (199)
Q Consensus 19 ppG~rF~-PTDeELv~~Y 35 (199)
--||+|+ ||=++.+.+-
T Consensus 30 ~~GF~F~~p~l~~AL~~l 47 (48)
T PF08338_consen 30 EAGFQFRYPTLEEALRDL 47 (48)
T ss_dssp HTT---S-SSHHHHHHH-
T ss_pred HCCCcccCCCHHHHHhcc
Confidence 3599998 8888877653
No 12
>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=26.92 E-value=47 Score=16.24 Aligned_cols=8 Identities=25% Similarity=0.667 Sum_probs=6.3
Q ss_pred CCeEEEEe
Q 038703 74 PDEGYFFT 81 (199)
Q Consensus 74 ~~~wyFF~ 81 (199)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 47899993
No 13
>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=26.82 E-value=34 Score=29.16 Aligned_cols=28 Identities=18% Similarity=0.075 Sum_probs=18.1
Q ss_pred CCCCCCCcceECCChHHHHHHHHHHHHhCC
Q 038703 14 EEFDLPLGYRFSPNGQEIIVQYLTKKILNQ 43 (199)
Q Consensus 14 ~~~~lppG~rF~PTDeELv~~YL~~ki~g~ 43 (199)
+.+-+||-| |.||++||+.|| ..-+...
T Consensus 99 ~v~~~~P~y-~~~~~~~i~~~~-~~v~~a~ 126 (288)
T cd00954 99 AISAITPFY-YKFSFEEIKDYY-REIIAAA 126 (288)
T ss_pred EEEEeCCCC-CCCCHHHHHHHH-HHHHHhc
Confidence 344456654 889999999865 4444444
No 14
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=26.08 E-value=39 Score=29.01 Aligned_cols=31 Identities=10% Similarity=0.133 Sum_probs=20.2
Q ss_pred CCCCCCCCCCcceECCChHHHHHHHHHHHHhCC
Q 038703 11 NQEEEFDLPLGYRFSPNGQEIIVQYLTKKILNQ 43 (199)
Q Consensus 11 ~~~~~~~lppG~rF~PTDeELv~~YL~~ki~g~ 43 (199)
.-.+.+-+||-| |.|++++|+.|| +.-+...
T Consensus 95 Gad~v~v~pP~y-~~~~~~~l~~~f-~~ia~a~ 125 (294)
T TIGR02313 95 GADAAMVIVPYY-NKPNQEALYDHF-AEVADAV 125 (294)
T ss_pred CCCEEEEcCccC-CCCCHHHHHHHH-HHHHHhc
Confidence 334455667665 899999999865 4444433
No 15
>KOG3238 consensus Chloride ion current inducer protein [Inorganic ion transport and metabolism]
Probab=24.88 E-value=85 Score=25.90 Aligned_cols=50 Identities=18% Similarity=0.233 Sum_probs=28.8
Q ss_pred CCCCCCcceECCChHHHHHHHHHHHHhCCCCCCCceeecccCCCCCCCCCC
Q 038703 15 EFDLPLGYRFSPNGQEIIVQYLTKKILNQRLPSNIIKDIDLYAYDHPRQLP 65 (199)
Q Consensus 15 ~~~lppG~rF~PTDeELv~~YL~~ki~g~~l~~~~I~~~Dvy~~~~P~~Lp 65 (199)
....--+|||+|+|.--+..---.....+.+-+....+.|-|.-+ =|+.-
T Consensus 106 dve~i~e~rfvpsDk~~l~a~f~qfcecqel~p~P~ED~~~~dge-e~~me 155 (216)
T KOG3238|consen 106 DVEPITEFRFVPSDKSALEAMFTQFCECQELNPDPDEDEDDYDGE-EYDME 155 (216)
T ss_pred cccccccceecCCchhHHHHHHHHHHhhhhcCCCccccccccccc-hhhhh
Confidence 345566899999998776643333334433322224555666655 55554
No 16
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=22.57 E-value=51 Score=28.01 Aligned_cols=34 Identities=12% Similarity=0.150 Sum_probs=21.0
Q ss_pred CCCCCCCCCCcceECCChHHHHHHHHHHHHhCCCCC
Q 038703 11 NQEEEFDLPLGYRFSPNGQEIIVQYLTKKILNQRLP 46 (199)
Q Consensus 11 ~~~~~~~lppG~rF~PTDeELv~~YL~~ki~g~~l~ 46 (199)
.-.+.+-+||=| |.||++||+.||. .-+..-++|
T Consensus 93 Gad~v~v~pP~y-~~~~~~~i~~~~~-~i~~~~~~p 126 (285)
T TIGR00674 93 GADGFLVVTPYY-NKPTQEGLYQHFK-AIAEEVDLP 126 (285)
T ss_pred CCCEEEEcCCcC-CCCCHHHHHHHHH-HHHhcCCCC
Confidence 334455667665 7899999998654 333333343
No 17
>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=21.74 E-value=91 Score=25.31 Aligned_cols=21 Identities=33% Similarity=0.464 Sum_probs=14.6
Q ss_pred ChHHHHHHHH--HHHHhCCCCCC
Q 038703 27 NGQEIIVQYL--TKKILNQRLPS 47 (199)
Q Consensus 27 TDeELv~~YL--~~ki~g~~l~~ 47 (199)
+|||||.||- .++..|...+.
T Consensus 6 sDe~Li~yY~~L~K~~g~~~~~~ 28 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGSDVPS 28 (186)
T ss_pred cHHHHHHHHHHHHHHhCCCCCCc
Confidence 7999999984 55555554443
No 18
>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=21.60 E-value=86 Score=26.45 Aligned_cols=34 Identities=12% Similarity=0.176 Sum_probs=22.4
Q ss_pred CCCCCCCCCCcceECCChHHHHHHHHHHHHhCCCCC
Q 038703 11 NQEEEFDLPLGYRFSPNGQEIIVQYLTKKILNQRLP 46 (199)
Q Consensus 11 ~~~~~~~lppG~rF~PTDeELv~~YL~~ki~g~~l~ 46 (199)
.-.+.+-+||.| |.||++||+. |.+.-+...++|
T Consensus 95 G~d~v~~~~P~~-~~~~~~~l~~-~~~~ia~~~~~p 128 (284)
T cd00950 95 GADAALVVTPYY-NKPSQEGLYA-HFKAIAEATDLP 128 (284)
T ss_pred CCCEEEEccccc-CCCCHHHHHH-HHHHHHhcCCCC
Confidence 334456677855 8899999997 555555544444
No 19
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=21.52 E-value=1.2e+02 Score=21.74 Aligned_cols=37 Identities=19% Similarity=0.354 Sum_probs=28.4
Q ss_pred CCChHHHHHHHHHHHHhCCCCCCCceeecccCCCCCCCCCCc
Q 038703 25 SPNGQEIIVQYLTKKILNQRLPSNIIKDIDLYAYDHPRQLPI 66 (199)
Q Consensus 25 ~PTDeELv~~YL~~ki~g~~l~~~~I~~~Dvy~~~~P~~Lp~ 66 (199)
+-|..||++.-...-..|+|||.+ .|+-... |.+||.
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~D----~Dl~K~~-~d~iP~ 86 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPDD----ADLRKER-SDEIPE 86 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcC-cccccH
Confidence 456778888777778899999964 5777767 888884
No 20
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=21.11 E-value=1.3e+02 Score=21.63 Aligned_cols=37 Identities=22% Similarity=0.417 Sum_probs=22.3
Q ss_pred CCChHHHHHHHHHHHHhCCCCCCCceeecccCCCCCCCCCCc
Q 038703 25 SPNGQEIIVQYLTKKILNQRLPSNIIKDIDLYAYDHPRQLPI 66 (199)
Q Consensus 25 ~PTDeELv~~YL~~ki~g~~l~~~~I~~~Dvy~~~~P~~Lp~ 66 (199)
+-|..||++.-...-..|+|||.+ .|+-... |..+|.
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~D----~dl~kd~-~d~ip~ 86 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPTD----DDLRKDR-PDEIPA 86 (104)
T ss_dssp S-SHHHHHHHHHHHHHH------T----TGGGSTS-GSSS-H
T ss_pred hcccHHHHHHHHHHHhcCCCCCCh----hhhhhcC-CccchH
Confidence 457788888777788899999964 5777777 888884
Done!