Query 043911
Match_columns 89
No_of_seqs 106 out of 674
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 09:28:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043911.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043911hhsearch_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 1.8E-35 4E-40 193.7 2.2 83 3-89 1-86 (129)
2 PHA00692 hypothetical protein 71.4 1.5 3.3E-05 25.7 0.3 10 2-11 36-45 (74)
3 PF07960 CBP4: CBP4; InterPro 68.9 2.7 5.9E-05 27.9 1.1 11 10-20 30-40 (128)
4 smart00265 BH4 BH4 Bcl-2 homol 63.4 11 0.00023 18.5 2.3 18 11-28 3-20 (27)
5 PLN02417 dihydrodipicolinate s 60.4 5.5 0.00012 28.9 1.5 18 3-21 103-120 (280)
6 cd00954 NAL N-Acetylneuraminic 59.6 5.5 0.00012 28.9 1.4 19 3-22 103-121 (288)
7 TIGR02313 HpaI-NOT-DapA 2,4-di 58.9 6.2 0.00013 28.9 1.5 18 3-21 102-119 (294)
8 PF13822 ACC_epsilon: Acyl-CoA 57.3 5.8 0.00013 22.8 0.9 9 10-18 10-18 (62)
9 PF01473 CW_binding_1: Putativ 57.0 8.8 0.00019 16.6 1.3 8 58-65 7-14 (19)
10 smart00707 RPEL Repeat in Dros 55.7 8.8 0.00019 18.6 1.3 13 7-19 7-19 (26)
11 cd00952 CHBPH_aldolase Trans-o 54.6 7.6 0.00017 28.7 1.4 17 3-20 110-126 (309)
12 TIGR00674 dapA dihydrodipicoli 51.8 11 0.00023 27.4 1.8 19 3-22 100-118 (285)
13 PF07131 DUF1382: Protein of u 51.8 11 0.00024 21.9 1.5 14 5-18 22-39 (61)
14 cd00950 DHDPS Dihydrodipicolin 51.1 9.8 0.00021 27.4 1.5 17 3-20 102-118 (284)
15 PRK03170 dihydrodipicolinate s 50.7 11 0.00023 27.4 1.6 17 3-20 103-119 (292)
16 PRK04147 N-acetylneuraminate l 47.7 12 0.00025 27.3 1.5 17 4-21 107-123 (293)
17 TIGR03249 KdgD 5-dehydro-4-deo 44.7 15 0.00032 26.9 1.6 18 3-21 106-123 (296)
18 cd00408 DHDPS-like Dihydrodipi 42.5 17 0.00036 26.0 1.6 18 3-21 99-116 (281)
19 PF02180 BH4: Bcl-2 homology r 42.0 26 0.00056 17.2 1.7 17 12-28 4-20 (27)
20 PF02755 RPEL: RPEL repeat; I 40.3 18 0.00038 17.4 1.0 11 9-19 9-19 (26)
21 PRK03620 5-dehydro-4-deoxygluc 37.4 21 0.00045 26.2 1.5 19 3-22 108-126 (303)
22 PF02375 JmjN: jmjN domain; I 36.0 18 0.00039 18.5 0.7 10 9-18 3-12 (34)
23 PF00701 DHDPS: Dihydrodipicol 33.0 17 0.00037 26.2 0.4 17 4-21 104-120 (289)
24 COG2326 Uncharacterized conser 32.1 35 0.00075 25.4 1.9 32 4-37 100-135 (270)
25 PF13145 Rotamase_2: PPIC-type 31.4 37 0.00081 20.1 1.7 16 11-26 1-16 (121)
26 PF04700 Baculo_gp41: Structur 30.9 31 0.00067 24.3 1.4 17 12-28 6-24 (186)
27 PF03540 TFIID_30kDa: Transcri 29.9 40 0.00087 18.8 1.5 11 13-23 4-14 (51)
28 COG0020 UppS Undecaprenyl pyro 28.0 40 0.00086 24.6 1.6 34 13-50 172-210 (245)
29 PF05891 Methyltransf_PK: AdoM 26.5 43 0.00094 24.1 1.5 29 10-42 134-165 (218)
30 PHA00733 hypothetical protein 26.2 47 0.001 21.6 1.6 16 4-19 16-31 (128)
31 PF08990 Docking: Erythronolid 26.2 36 0.00078 16.5 0.8 12 12-24 3-14 (27)
32 TIGR03874 4cys_cytochr c-type 25.5 60 0.0013 21.8 2.0 23 5-28 93-119 (143)
33 PF02436 PYC_OADA: Conserved c 25.0 52 0.0011 23.1 1.7 19 10-28 135-153 (196)
34 TIGR00683 nanA N-acetylneurami 23.7 51 0.0011 24.1 1.5 16 7-22 106-121 (290)
35 cd00490 Met_repressor_MetJ Met 22.5 1E+02 0.0022 19.4 2.5 39 10-52 50-88 (103)
36 cd00951 KDGDH 5-dehydro-4-deox 22.5 63 0.0014 23.5 1.8 16 4-20 102-117 (289)
37 PF06214 SLAM: Signaling lymph 21.9 29 0.00064 22.8 -0.1 30 38-67 93-123 (126)
38 PF15374 CCDC71L: Coiled-coil 21.2 1E+02 0.0023 24.0 2.8 40 4-47 29-70 (376)
39 PF09758 FPL: Uncharacterised 21.0 47 0.001 22.5 0.8 16 7-22 79-94 (149)
40 PF12746 GNAT_acetyltran: GNAT 20.9 73 0.0016 23.4 1.8 20 2-21 124-143 (265)
41 PF08672 APC2: Anaphase promot 20.8 64 0.0014 18.4 1.2 19 9-28 31-49 (60)
42 COG4802 FtrB Ferredoxin-thiore 20.4 93 0.002 20.1 2.0 22 5-27 20-41 (110)
43 PRK05264 transcriptional repre 20.2 1.2E+02 0.0025 19.3 2.4 39 10-52 51-89 (105)
44 PF12189 VirE1: Single-strand 20.1 31 0.00067 20.0 -0.2 24 8-35 35-58 (62)
45 PF07735 FBA_2: F-box associat 20.1 97 0.0021 17.2 1.9 16 12-28 45-60 (70)
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=1.8e-35 Score=193.75 Aligned_cols=83 Identities=35% Similarity=0.592 Sum_probs=55.1
Q ss_pred CCCCceecCChHHHHHHHHHhhhCCCCCCCCc-ceE--eeCCCCCCCchhhhccCCCCCceEEEEeccccccCCCCcccc
Q 043911 3 SLMGFRFQPSNEQIICLLEKKRLNPRFLHHTI-KDI--DDICSLEPWDLAGASKTESEDQVCYFFYKPYYKYKESTRAHR 79 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~YL~~Ki~g~~~~~~~-~~I--~Dvy~~~Pw~L~~~~~~~~~~~~wYFF~~~~~k~~~g~R~~R 79 (89)
|||||||+|||+|||.+||++|+.|+ +++. ++| +|||+.|||+|+.... .++++|||||++++++.+|.|.+|
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~--~~~~~~~i~~~Diy~~~P~~L~~~~~--~~~~~~yFF~~~~~~~~~~~r~~R 76 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGE--PLPCEDVIHDVDIYSAHPWELPAKFK--GGDEEWYFFSPRKKKYPNGGRPNR 76 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT---HHCS-CHSEE--GGGS-GGGCHHHSS--S-SSEEEEEEE----------S-E
T ss_pred CCCceEecCChHHHHHHHHHHHhcCC--CCCcccceeecccCccChHHhhhhcc--CCCceEEEEEecccccCCcccccc
Confidence 79999999999999999999999999 7777 566 9999999999995332 267799999999999999999999
Q ss_pred cCCCceeecC
Q 043911 80 RTNAGYWKVT 89 (89)
Q Consensus 80 ~~~~G~Wk~t 89 (89)
++++|+||++
T Consensus 77 ~~~~G~Wk~~ 86 (129)
T PF02365_consen 77 VTGGGYWKST 86 (129)
T ss_dssp EETTEEEEEE
T ss_pred cccceEEeec
Confidence 9999999974
No 2
>PHA00692 hypothetical protein
Probab=71.41 E-value=1.5 Score=25.66 Aligned_cols=10 Identities=50% Similarity=0.657 Sum_probs=7.9
Q ss_pred CCCCCceecC
Q 043911 2 ESLMGFRFQP 11 (89)
Q Consensus 2 ~lp~GfrF~P 11 (89)
+.||||||--
T Consensus 36 eyppgfrfgg 45 (74)
T PHA00692 36 EYPPGFRFGG 45 (74)
T ss_pred ecCCCccccc
Confidence 5799999953
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=68.92 E-value=2.7 Score=27.92 Aligned_cols=11 Identities=18% Similarity=0.428 Sum_probs=9.8
Q ss_pred cCChHHHHHHH
Q 043911 10 QPSNEQIICLL 20 (89)
Q Consensus 10 ~PTDeELi~~Y 20 (89)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 69999999875
No 4
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=63.43 E-value=11 Score=18.54 Aligned_cols=18 Identities=11% Similarity=0.183 Sum_probs=15.5
Q ss_pred CChHHHHHHHHHhhhCCC
Q 043911 11 PSNEQIICLLEKKRLNPR 28 (89)
Q Consensus 11 PTDeELi~~YL~~Ki~g~ 28 (89)
.+-.|||..|+.-|+..+
T Consensus 3 ~~nRelV~~yv~yKLsQr 20 (27)
T smart00265 3 LDNRELVVDYVTYKLSQN 20 (27)
T ss_pred cchHHHHHHHHHHHHhhc
Confidence 356899999999999877
No 5
>PLN02417 dihydrodipicolinate synthase
Probab=60.41 E-value=5.5 Score=28.94 Aligned_cols=18 Identities=22% Similarity=0.108 Sum_probs=14.2
Q ss_pred CCCCceecCChHHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLLE 21 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~YL 21 (89)
.|| +.|.||++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 466 458999999999873
No 6
>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=59.55 E-value=5.5 Score=28.94 Aligned_cols=19 Identities=16% Similarity=0.036 Sum_probs=14.0
Q ss_pred CCCCceecCChHHHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLLEK 22 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~YL~ 22 (89)
+||-| |.||++||+.||..
T Consensus 103 ~~P~y-~~~~~~~i~~~~~~ 121 (288)
T cd00954 103 ITPFY-YKFSFEEIKDYYRE 121 (288)
T ss_pred eCCCC-CCCCHHHHHHHHHH
Confidence 35544 78999999997743
No 7
>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=58.89 E-value=6.2 Score=28.93 Aligned_cols=18 Identities=11% Similarity=0.163 Sum_probs=14.2
Q ss_pred CCCCceecCChHHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLLE 21 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~YL 21 (89)
+||-| |.|+++||+.||-
T Consensus 102 ~pP~y-~~~~~~~l~~~f~ 119 (294)
T TIGR02313 102 IVPYY-NKPNQEALYDHFA 119 (294)
T ss_pred cCccC-CCCCHHHHHHHHH
Confidence 45654 8899999999874
No 8
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=57.28 E-value=5.8 Score=22.81 Aligned_cols=9 Identities=22% Similarity=0.733 Sum_probs=7.5
Q ss_pred cCChHHHHH
Q 043911 10 QPSNEQIIC 18 (89)
Q Consensus 10 ~PTDeELi~ 18 (89)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 799999854
No 9
>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=57.05 E-value=8.8 Score=16.64 Aligned_cols=8 Identities=25% Similarity=0.629 Sum_probs=6.6
Q ss_pred CceEEEEe
Q 043911 58 DQVCYFFY 65 (89)
Q Consensus 58 ~~~wYFF~ 65 (89)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 58999994
No 10
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=55.72 E-value=8.8 Score=18.63 Aligned_cols=13 Identities=15% Similarity=0.266 Sum_probs=10.7
Q ss_pred ceecCChHHHHHH
Q 043911 7 FRFQPSNEQIICL 19 (89)
Q Consensus 7 frF~PTDeELi~~ 19 (89)
...+||-+|||..
T Consensus 7 l~~RP~~eeLv~r 19 (26)
T smart00707 7 LSQRPTREELEER 19 (26)
T ss_pred HHcCCCHHHHHHc
Confidence 4578999999973
No 11
>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=54.63 E-value=7.6 Score=28.69 Aligned_cols=17 Identities=0% Similarity=-0.033 Sum_probs=14.1
Q ss_pred CCCCceecCChHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLL 20 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~Y 20 (89)
+|| +.|.||++||+.||
T Consensus 110 ~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 110 GRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred CCC-cCCCCCHHHHHHHH
Confidence 566 56889999999987
No 12
>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=51.84 E-value=11 Score=27.35 Aligned_cols=19 Identities=11% Similarity=0.139 Sum_probs=14.3
Q ss_pred CCCCceecCChHHHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLLEK 22 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~YL~ 22 (89)
+||-| |.||++||+.||..
T Consensus 100 ~pP~y-~~~~~~~i~~~~~~ 118 (285)
T TIGR00674 100 VTPYY-NKPTQEGLYQHFKA 118 (285)
T ss_pred cCCcC-CCCCHHHHHHHHHH
Confidence 45554 78999999997743
No 13
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=51.80 E-value=11 Score=21.90 Aligned_cols=14 Identities=36% Similarity=0.838 Sum_probs=11.2
Q ss_pred CCceecC----ChHHHHH
Q 043911 5 MGFRFQP----SNEQIIC 18 (89)
Q Consensus 5 ~GfrF~P----TDeELi~ 18 (89)
.|+||.| ||+|+..
T Consensus 22 ~GIRFVpiPv~~dee~~~ 39 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHT 39 (61)
T ss_pred cCceeeccccccHHHHHH
Confidence 5999999 7887654
No 14
>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=51.09 E-value=9.8 Score=27.35 Aligned_cols=17 Identities=18% Similarity=0.210 Sum_probs=13.4
Q ss_pred CCCCceecCChHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLL 20 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~Y 20 (89)
+||.| |.||++||+.||
T Consensus 102 ~~P~~-~~~~~~~l~~~~ 118 (284)
T cd00950 102 VTPYY-NKPSQEGLYAHF 118 (284)
T ss_pred ccccc-CCCCHHHHHHHH
Confidence 46654 889999999965
No 15
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=50.74 E-value=11 Score=27.40 Aligned_cols=17 Identities=12% Similarity=0.139 Sum_probs=13.6
Q ss_pred CCCCceecCChHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLL 20 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~Y 20 (89)
+||-| |.|+++||+.||
T Consensus 103 ~pP~~-~~~~~~~i~~~~ 119 (292)
T PRK03170 103 VTPYY-NKPTQEGLYQHF 119 (292)
T ss_pred CCCcC-CCCCHHHHHHHH
Confidence 46655 889999999976
No 16
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=47.67 E-value=12 Score=27.31 Aligned_cols=17 Identities=18% Similarity=-0.097 Sum_probs=13.0
Q ss_pred CCCceecCChHHHHHHHH
Q 043911 4 LMGFRFQPSNEQIICLLE 21 (89)
Q Consensus 4 p~GfrF~PTDeELi~~YL 21 (89)
||. -|.||++||+.||-
T Consensus 107 ~P~-y~~~~~~~l~~~f~ 123 (293)
T PRK04147 107 TPF-YYPFSFEEICDYYR 123 (293)
T ss_pred CCc-CCCCCHHHHHHHHH
Confidence 444 48899999999763
No 17
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=44.73 E-value=15 Score=26.85 Aligned_cols=18 Identities=11% Similarity=0.109 Sum_probs=13.6
Q ss_pred CCCCceecCChHHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLLE 21 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~YL 21 (89)
+|| |-|.||++||+.||-
T Consensus 106 ~pP-~y~~~s~~~i~~~f~ 123 (296)
T TIGR03249 106 LPP-YLINGEQEGLYAHVE 123 (296)
T ss_pred CCC-CCCCCCHHHHHHHHH
Confidence 455 447799999999763
No 18
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=42.52 E-value=17 Score=26.02 Aligned_cols=18 Identities=22% Similarity=0.294 Sum_probs=13.1
Q ss_pred CCCCceecCChHHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLLE 21 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~YL 21 (89)
+||-| |.||++|++.||-
T Consensus 99 ~pP~y-~~~~~~~~~~~~~ 116 (281)
T cd00408 99 VPPYY-NKPSQEGIVAHFK 116 (281)
T ss_pred CCCcC-CCCCHHHHHHHHH
Confidence 35544 6699999999753
No 19
>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=42.00 E-value=26 Score=17.17 Aligned_cols=17 Identities=18% Similarity=0.251 Sum_probs=14.3
Q ss_pred ChHHHHHHHHHhhhCCC
Q 043911 12 SNEQIICLLEKKRLNPR 28 (89)
Q Consensus 12 TDeELi~~YL~~Ki~g~ 28 (89)
+-.|||..|+.-|+..+
T Consensus 4 ~nR~lV~~yi~yKLsQr 20 (27)
T PF02180_consen 4 DNRELVEDYISYKLSQR 20 (27)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred cHHHHHHHHHHHHhhhc
Confidence 45799999999998766
No 20
>PF02755 RPEL: RPEL repeat; InterPro: IPR004018 The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that Q9VZY2 from SWISSPROT contains a SAP domain that is also implicated in DNA binding.; PDB: 2YJE_M 2V52_M 2YJF_M 2V51_E.
Probab=40.31 E-value=18 Score=17.45 Aligned_cols=11 Identities=18% Similarity=0.434 Sum_probs=6.4
Q ss_pred ecCChHHHHHH
Q 043911 9 FQPSNEQIICL 19 (89)
Q Consensus 9 F~PTDeELi~~ 19 (89)
.+|+-+|||..
T Consensus 9 ~RP~~~eLv~r 19 (26)
T PF02755_consen 9 QRPTREELVER 19 (26)
T ss_dssp T---HHHHHHT
T ss_pred cCCCHHHHHHc
Confidence 47999999873
No 21
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=37.40 E-value=21 Score=26.21 Aligned_cols=19 Identities=11% Similarity=0.093 Sum_probs=14.3
Q ss_pred CCCCceecCChHHHHHHHHH
Q 043911 3 SLMGFRFQPSNEQIICLLEK 22 (89)
Q Consensus 3 lp~GfrF~PTDeELi~~YL~ 22 (89)
+|| +.|.||+++|+.||-.
T Consensus 108 ~pP-~y~~~~~~~i~~~f~~ 126 (303)
T PRK03620 108 LPP-YLTEAPQEGLAAHVEA 126 (303)
T ss_pred CCC-CCCCCCHHHHHHHHHH
Confidence 355 5678999999997643
No 22
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=35.97 E-value=18 Score=18.47 Aligned_cols=10 Identities=30% Similarity=0.441 Sum_probs=4.8
Q ss_pred ecCChHHHHH
Q 043911 9 FQPSNEQIIC 18 (89)
Q Consensus 9 F~PTDeELi~ 18 (89)
|+||.||--+
T Consensus 3 f~Pt~eEF~d 12 (34)
T PF02375_consen 3 FYPTMEEFKD 12 (34)
T ss_dssp E---HHHHS-
T ss_pred ccCCHHHHhC
Confidence 8899999744
No 23
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=32.97 E-value=17 Score=26.24 Aligned_cols=17 Identities=29% Similarity=0.567 Sum_probs=13.4
Q ss_pred CCCceecCChHHHHHHHH
Q 043911 4 LMGFRFQPSNEQIICLLE 21 (89)
Q Consensus 4 p~GfrF~PTDeELi~~YL 21 (89)
|| +.+.||++||+.||-
T Consensus 104 ~P-~~~~~s~~~l~~y~~ 120 (289)
T PF00701_consen 104 PP-YYFKPSQEELIDYFR 120 (289)
T ss_dssp ES-TSSSCCHHHHHHHHH
T ss_pred cc-ccccchhhHHHHHHH
Confidence 44 557899999999773
No 24
>COG2326 Uncharacterized conserved protein [Function unknown]
Probab=32.14 E-value=35 Score=25.44 Aligned_cols=32 Identities=9% Similarity=-0.001 Sum_probs=23.0
Q ss_pred CCCcee----cCChHHHHHHHHHhhhCCCCCCCCcceE
Q 043911 4 LMGFRF----QPSNEQIICLLEKKRLNPRFLHHTIKDI 37 (89)
Q Consensus 4 p~GfrF----~PTDeELi~~YL~~Ki~g~~~~~~~~~I 37 (89)
|-|+|= .|||+|+-..||.+-+.-- |--..|+
T Consensus 100 PR~~rvval~aPt~~E~~qwY~qRy~~~l--Pa~Geiv 135 (270)
T COG2326 100 PRGARVVALPAPTDRERGQWYFQRYVAHL--PAAGEIV 135 (270)
T ss_pred CceeEEeecCCCChHhhccHHHHHHHHhC--CCCCeEE
Confidence 445553 5999999999999999855 4333444
No 25
>PF13145 Rotamase_2: PPIC-type PPIASE domain; PDB: 3NRK_A 2KGJ_A.
Probab=31.39 E-value=37 Score=20.13 Aligned_cols=16 Identities=13% Similarity=0.239 Sum_probs=9.3
Q ss_pred CChHHHHHHHHHhhhC
Q 043911 11 PSNEQIICLLEKKRLN 26 (89)
Q Consensus 11 PTDeELi~~YL~~Ki~ 26 (89)
|||+||-.+|-.++-.
T Consensus 1 vte~el~~yY~~n~~~ 16 (121)
T PF13145_consen 1 VTEEELRAYYEENKDR 16 (121)
T ss_dssp --HHHHHHHHHH-HHH
T ss_pred CCHHHHHHHHHHHHHH
Confidence 6778887777766554
No 26
>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=30.86 E-value=31 Score=24.34 Aligned_cols=17 Identities=24% Similarity=0.323 Sum_probs=12.5
Q ss_pred ChHHHHHHH--HHhhhCCC
Q 043911 12 SNEQIICLL--EKKRLNPR 28 (89)
Q Consensus 12 TDeELi~~Y--L~~Ki~g~ 28 (89)
+|||||.|| |.+|..|.
T Consensus 6 sDe~Li~yY~~L~K~~g~~ 24 (186)
T PF04700_consen 6 SDEELIEYYANLEKKYGGS 24 (186)
T ss_pred cHHHHHHHHHHHHHHhCCC
Confidence 899999998 44455554
No 27
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=29.91 E-value=40 Score=18.84 Aligned_cols=11 Identities=0% Similarity=0.120 Sum_probs=9.1
Q ss_pred hHHHHHHHHHh
Q 043911 13 NEQIICLLEKK 23 (89)
Q Consensus 13 DeELi~~YL~~ 23 (89)
.+||+.|||..
T Consensus 4 PD~v~~~yL~~ 14 (51)
T PF03540_consen 4 PDEVTDYYLER 14 (51)
T ss_pred CHHHHHHHHHH
Confidence 47899999975
No 28
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism]
Probab=27.99 E-value=40 Score=24.59 Aligned_cols=34 Identities=15% Similarity=0.090 Sum_probs=25.7
Q ss_pred hHHHHHHHHHhhhCCCCCCCCcceE-----eeCCCCCCCchhh
Q 043911 13 NEQIICLLEKKRLNPRFLHHTIKDI-----DDICSLEPWDLAG 50 (89)
Q Consensus 13 DeELi~~YL~~Ki~g~~~~~~~~~I-----~Dvy~~~Pw~L~~ 50 (89)
|||+|..||.. .+. |.|.-+| ..+..+=||++.-
T Consensus 172 ~e~~i~~~L~~--~~~--pdpDLlIRTsGe~RlSnFllWQ~aY 210 (245)
T COG0020 172 DEELISSHLYT--SGL--PDPDLLIRTSGEQRLSNFLLWQSAY 210 (245)
T ss_pred CHHHHHHhhcc--cCC--CCCCEEEeCCCcccccccHHHHHHh
Confidence 68999999998 555 5444456 7888999998754
No 29
>PF05891 Methyltransf_PK: AdoMet dependent proline di-methyltransferase; InterPro: IPR008576 This family consists of several eukaryotic proteins of unknown function that are S-adenosyl-L-methionine-dependent methyltransferase-like.; GO: 0008168 methyltransferase activity; PDB: 1XTP_A 2EX4_B.
Probab=26.50 E-value=43 Score=24.10 Aligned_cols=29 Identities=14% Similarity=0.247 Sum_probs=17.0
Q ss_pred cCChHHHHHHHHHhhhCCCCCCCCcceE---eeCCC
Q 043911 10 QPSNEQIICLLEKKRLNPRFLHHTIKDI---DDICS 42 (89)
Q Consensus 10 ~PTDeELi~~YL~~Ki~g~~~~~~~~~I---~Dvy~ 42 (89)
+=||++||. ||++=..+- -|..+| .||..
T Consensus 134 hLTD~dlv~-fL~RCk~~L---~~~G~IvvKEN~~~ 165 (218)
T PF05891_consen 134 HLTDEDLVA-FLKRCKQAL---KPNGVIVVKENVSS 165 (218)
T ss_dssp GS-HHHHHH-HHHHHHHHE---EEEEEEEEEEEEES
T ss_pred cCCHHHHHH-HHHHHHHhC---cCCcEEEEEecCCC
Confidence 348999999 677643333 134544 67654
No 30
>PHA00733 hypothetical protein
Probab=26.19 E-value=47 Score=21.57 Aligned_cols=16 Identities=13% Similarity=0.081 Sum_probs=14.0
Q ss_pred CCCceecCChHHHHHH
Q 043911 4 LMGFRFQPSNEQIICL 19 (89)
Q Consensus 4 p~GfrF~PTDeELi~~ 19 (89)
-+|+-|+||-|||-.|
T Consensus 16 ~~~~~~~~~~~~~~~~ 31 (128)
T PHA00733 16 HKGIFIHVTLEELKRY 31 (128)
T ss_pred CCCeEEecCHHHhhhh
Confidence 5799999999999774
No 31
>PF08990 Docking: Erythronolide synthase docking; InterPro: IPR015083 The N-terminal docking domain found in modular polyketide synthase assumes an alpha-helical structure, wherein two alpha-helices are connected by a short loop. Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function []. ; GO: 0016740 transferase activity, 0048037 cofactor binding; PDB: 2HG4_E.
Probab=26.19 E-value=36 Score=16.55 Aligned_cols=12 Identities=8% Similarity=0.121 Sum_probs=7.3
Q ss_pred ChHHHHHHHHHhh
Q 043911 12 SNEQIICLLEKKR 24 (89)
Q Consensus 12 TDeELi~~YL~~K 24 (89)
+++.|.. ||++=
T Consensus 3 ~e~kLr~-YLkr~ 14 (27)
T PF08990_consen 3 NEDKLRD-YLKRV 14 (27)
T ss_dssp -HCHHHH-HHHHH
T ss_pred cHHHHHH-HHHHH
Confidence 4566655 88864
No 32
>TIGR03874 4cys_cytochr c-type cytochrome, methanol metabolism-related. This family represents a c-type cytochrome related to (but excluding) cytochrome c-555 of Methylococcus capsulatus. Members contain four invariant Cys residues, including two from a heme-binding motif shared with c-555, and two others.
Probab=25.47 E-value=60 Score=21.84 Aligned_cols=23 Identities=13% Similarity=0.098 Sum_probs=18.3
Q ss_pred CCceecCChH----HHHHHHHHhhhCCC
Q 043911 5 MGFRFQPSNE----QIICLLEKKRLNPR 28 (89)
Q Consensus 5 ~GfrF~PTDe----ELi~~YL~~Ki~g~ 28 (89)
|+|.-..+|+ +|+. ||+....|.
T Consensus 93 PaF~~~LsD~~eIa~L~~-YLR~~~~g~ 119 (143)
T TIGR03874 93 PAFGDNPNVMCYLDDLYV-YLRARGTDA 119 (143)
T ss_pred CCccccCCcHHHHHHHHH-HHHhccCCC
Confidence 7898899987 4444 899888887
No 33
>PF02436 PYC_OADA: Conserved carboxylase domain; InterPro: IPR003379 This domain represents a conserved region in pyruvate carboxylase (PYC) (6.4.1.1 from EC), oxaloacetate decarboxylase alpha chain (OADA) (4.1.1.3 from EC), and transcarboxylase 5s subunit (2.1.3.1 from EC). The domain is found adjacent to the HMGL-like domain (IPR000891 from INTERPRO) and often close to the biotin_lipoyl domain (IPR000089 from INTERPRO) of biotin requiring enzymes.; PDB: 2NX9_B 3HBL_A 3HB9_C 3HO8_A 3BG5_C 1S3H_A 1RQE_A 1U5J_A 1RQB_A 2QF7_B ....
Probab=25.03 E-value=52 Score=23.10 Aligned_cols=19 Identities=11% Similarity=0.335 Sum_probs=16.0
Q ss_pred cCChHHHHHHHHHhhhCCC
Q 043911 10 QPSNEQIICLLEKKRLNPR 28 (89)
Q Consensus 10 ~PTDeELi~~YL~~Ki~g~ 28 (89)
.+||||++.+-|.|++...
T Consensus 135 ~~~dedvlsyal~P~v~~~ 153 (196)
T PF02436_consen 135 EPTDEDVLSYALFPKVAED 153 (196)
T ss_dssp TSCHHHHHHHHHCHHHHHH
T ss_pred CCCHHHHHHHhcCchhHHH
Confidence 3799999999999998644
No 34
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=23.73 E-value=51 Score=24.06 Aligned_cols=16 Identities=19% Similarity=0.245 Sum_probs=12.7
Q ss_pred ceecCChHHHHHHHHH
Q 043911 7 FRFQPSNEQIICLLEK 22 (89)
Q Consensus 7 frF~PTDeELi~~YL~ 22 (89)
+.|.||++|++.||..
T Consensus 106 ~y~~~~~~~i~~yf~~ 121 (290)
T TIGR00683 106 FYYKFSFPEIKHYYDT 121 (290)
T ss_pred cCCCCCHHHHHHHHHH
Confidence 4578999999997753
No 35
>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=22.53 E-value=1e+02 Score=19.42 Aligned_cols=39 Identities=10% Similarity=0.159 Sum_probs=28.0
Q ss_pred cCChHHHHHHHHHhhhCCCCCCCCcceEeeCCCCCCCchhhhc
Q 043911 10 QPSNEQIICLLEKKRLNPRFLHHTIKDIDDICSLEPWDLAGAS 52 (89)
Q Consensus 10 ~PTDeELi~~YL~~Ki~g~~~~~~~~~I~Dvy~~~Pw~L~~~~ 52 (89)
|-|.-||++.-...-..|+ |+|.+ .|+-...|.++|+..
T Consensus 50 HATNSELLCEAFLHAfTGQ--PLP~D--~Dl~K~~~d~iP~~a 88 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQ--PLPDD--ADLRKERSDEIPEAA 88 (103)
T ss_pred hcccHHHHHHHHHHHhcCC--CCCCh--hhhhhcCcccccHHH
Confidence 3467788877666677888 88865 466777788887654
No 36
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=22.52 E-value=63 Score=23.49 Aligned_cols=16 Identities=6% Similarity=-0.099 Sum_probs=12.5
Q ss_pred CCCceecCChHHHHHHH
Q 043911 4 LMGFRFQPSNEQIICLL 20 (89)
Q Consensus 4 p~GfrF~PTDeELi~~Y 20 (89)
||- .|.|++++++.||
T Consensus 102 pP~-y~~~~~~~i~~~f 117 (289)
T cd00951 102 PPY-LTEAPQEGLYAHV 117 (289)
T ss_pred CCC-CCCCCHHHHHHHH
Confidence 444 4789999999976
No 37
>PF06214 SLAM: Signaling lymphocytic activation molecule (SLAM) protein; InterPro: IPR010407 This entry is found in several mammalian signalling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70 kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones []. SLAM has also been recognised as a receptor for Measles virus [].; GO: 0004872 receptor activity, 0046649 lymphocyte activation, 0009986 cell surface, 0016021 integral to membrane; PDB: 3ALX_D 3ALZ_B 3ALW_A.
Probab=21.87 E-value=29 Score=22.79 Aligned_cols=30 Identities=20% Similarity=0.190 Sum_probs=15.7
Q ss_pred eeCCCCCCCchhhhcc-CCCCCceEEEEecc
Q 043911 38 DDICSLEPWDLAGASK-TESEDQVCYFFYKP 67 (89)
Q Consensus 38 ~Dvy~~~Pw~L~~~~~-~~~~~~~wYFF~~~ 67 (89)
.|=|.+++..|.-.-. .+-+++-|||.+--
T Consensus 93 edgY~FhlEnLsL~Il~SrkE~EGWYfmtlE 123 (126)
T PF06214_consen 93 EDGYKFHLENLSLEILESRKEDEGWYFMTLE 123 (126)
T ss_dssp SSSEEEETTTTEEEETT--GGG-EEEEEEEE
T ss_pred ccccEEecccceeehhccccccCceEEEEee
Confidence 4556666666632110 12256789998743
No 38
>PF15374 CCDC71L: Coiled-coil domain-containing protein 71L
Probab=21.17 E-value=1e+02 Score=24.00 Aligned_cols=40 Identities=8% Similarity=0.093 Sum_probs=25.3
Q ss_pred CCCceecCChHHHHHHHHHhhhCCCCCCCCcceE--eeCCCCCCCc
Q 043911 4 LMGFRFQPSNEQIICLLEKKRLNPRFLHHTIKDI--DDICSLEPWD 47 (89)
Q Consensus 4 p~GfrF~PTDeELi~~YL~~Ki~g~~~~~~~~~I--~Dvy~~~Pw~ 47 (89)
|+--.|.=||.|||. ||.---..+ +...|. -|||++....
T Consensus 29 PmS~dl~~te~qLv~-Flq~Lr~eG---fqP~ILrSkDVYGYsSct 70 (376)
T PF15374_consen 29 PMSKDLSDTEAQLVA-FLQGLRHEG---FQPTILRSKDVYGYSSCT 70 (376)
T ss_pred ccccccchhHHHHHH-HHHHHhhcC---CCceeecccccccccccc
Confidence 444556669999999 677644433 223344 9999865543
No 39
>PF09758 FPL: Uncharacterised conserved protein; InterPro: IPR019155 The proteins in this family are functionally uncharacterised. They contain a highly conserved FPL motif.
Probab=21.03 E-value=47 Score=22.51 Aligned_cols=16 Identities=19% Similarity=0.447 Sum_probs=13.1
Q ss_pred ceecCChHHHHHHHHH
Q 043911 7 FRFQPSNEQIICLLEK 22 (89)
Q Consensus 7 frF~PTDeELi~~YL~ 22 (89)
+.|.-+|||++.+|.-
T Consensus 79 ~~~d~~~ee~l~yYIs 94 (149)
T PF09758_consen 79 YPFDFSDEEVLSYYIS 94 (149)
T ss_pred cCCCCCcchhHHHHHH
Confidence 5688889999999853
No 40
>PF12746 GNAT_acetyltran: GNAT acetyltransferase; PDB: 3G3S_B.
Probab=20.92 E-value=73 Score=23.42 Aligned_cols=20 Identities=10% Similarity=0.089 Sum_probs=14.5
Q ss_pred CCCCCceecCChHHHHHHHH
Q 043911 2 ESLMGFRFQPSNEQIICLLE 21 (89)
Q Consensus 2 ~lp~GfrF~PTDeELi~~YL 21 (89)
.||.||...+.|++|+..-+
T Consensus 124 ~lp~~y~l~~Ide~l~~~~~ 143 (265)
T PF12746_consen 124 ALPEGYELKRIDEELYENSL 143 (265)
T ss_dssp CS-TTCEEEE--HHHHHHHH
T ss_pred cCCCCeEEEECCHHHHHhhh
Confidence 47999999999999998654
No 41
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=20.77 E-value=64 Score=18.37 Aligned_cols=19 Identities=11% Similarity=0.128 Sum_probs=13.8
Q ss_pred ecCChHHHHHHHHHhhhCCC
Q 043911 9 FQPSNEQIICLLEKKRLNPR 28 (89)
Q Consensus 9 F~PTDeELi~~YL~~Ki~g~ 28 (89)
|..|.+||-. ||..++..+
T Consensus 31 ~~~s~~eL~~-fL~~lv~e~ 49 (60)
T PF08672_consen 31 YDISLEELQE-FLDRLVEEG 49 (60)
T ss_dssp TT--HHHHHH-HHHHHHHTT
T ss_pred CCCCHHHHHH-HHHHHHHCC
Confidence 4567888866 899999887
No 42
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=20.43 E-value=93 Score=20.08 Aligned_cols=22 Identities=14% Similarity=0.353 Sum_probs=13.9
Q ss_pred CCceecCChHHHHHHHHHhhhCC
Q 043911 5 MGFRFQPSNEQIICLLEKKRLNP 27 (89)
Q Consensus 5 ~GfrF~PTDeELi~~YL~~Ki~g 27 (89)
.|++|+|. -|++...|+.-+..
T Consensus 20 sG~~lnpD-~e~~~~v~~gL~~~ 41 (110)
T COG4802 20 SGYRLNPD-REFTAEVLRGLASN 41 (110)
T ss_pred cCceeCCC-HHHHHHHHHHHHHh
Confidence 59999995 45555456554443
No 43
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=20.19 E-value=1.2e+02 Score=19.28 Aligned_cols=39 Identities=10% Similarity=0.185 Sum_probs=27.8
Q ss_pred cCChHHHHHHHHHhhhCCCCCCCCcceEeeCCCCCCCchhhhc
Q 043911 10 QPSNEQIICLLEKKRLNPRFLHHTIKDIDDICSLEPWDLAGAS 52 (89)
Q Consensus 10 ~PTDeELi~~YL~~Ki~g~~~~~~~~~I~Dvy~~~Pw~L~~~~ 52 (89)
|-|.-||++.-...-..|+ |+|.+ .|+-...|.++|...
T Consensus 51 HATNSELLCEAFLHA~TGQ--PLP~D--~Dl~Kd~~d~ip~~a 89 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQ--PLPDD--EDLRKERSDEIPEAA 89 (105)
T ss_pred hcccHHHHHHHHHHHHcCC--CCCCh--hhhhhcCcccchHHH
Confidence 3467788877666677888 88865 466777788887653
No 44
>PF12189 VirE1: Single-strand DNA-binding protein; InterPro: IPR024237 The VirE1 family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length and contain a conserved IELE sequence motif. VirE1 is an acidic chaperone protein which binds to VirE2, a ssDNA binding protein []. These proteins are virulence factors of the plant pathogen Agrobacterium tumefaciens.; GO: 0005515 protein binding, 0006457 protein folding, 0009405 pathogenesis; PDB: 3BTP_B.
Probab=20.09 E-value=31 Score=20.01 Aligned_cols=24 Identities=8% Similarity=-0.060 Sum_probs=14.0
Q ss_pred eecCChHHHHHHHHHhhhCCCCCCCCcc
Q 043911 8 RFQPSNEQIICLLEKKRLNPRFLHHTIK 35 (89)
Q Consensus 8 rF~PTDeELi~~YL~~Ki~g~~~~~~~~ 35 (89)
-|.|-|-++|. |-.-++.. |+|.+
T Consensus 35 gFtslDL~mIE--LE~Fvl~c--PlP~~ 58 (62)
T PF12189_consen 35 GFTSLDLEMIE--LENFVLRC--PLPED 58 (62)
T ss_dssp TS-HHHHHHHH--HHHHHHT--------
T ss_pred CcccccHHHHH--HHHHHHhC--CCCcc
Confidence 47788999988 88888877 77653
No 45
>PF07735 FBA_2: F-box associated; InterPro: IPR012885 This domain is found is found towards the C terminus of proteins that contain an F-box, IPR001810 from INTERPRO, suggesting that they are effectors linked with ubiquitination.
Probab=20.07 E-value=97 Score=17.17 Aligned_cols=16 Identities=25% Similarity=0.277 Sum_probs=13.0
Q ss_pred ChHHHHHHHHHhhhCCC
Q 043911 12 SNEQIICLLEKKRLNPR 28 (89)
Q Consensus 12 TDeELi~~YL~~Ki~g~ 28 (89)
|.++|.. ||+.++.|.
T Consensus 45 t~~dln~-Flk~W~~G~ 60 (70)
T PF07735_consen 45 TNEDLNK-FLKHWINGS 60 (70)
T ss_pred CHHHHHH-HHHHHHcCC
Confidence 5677766 899999996
Done!