Query 040747
Match_columns 157
No_of_seqs 112 out of 992
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 11:23:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040747.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040747hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02365 NAM: No apical merist 100.0 8.2E-43 1.8E-47 253.0 4.5 118 12-131 1-129 (129)
2 PHA00692 hypothetical protein 53.1 5.1 0.00011 25.1 0.2 12 9-20 34-45 (74)
3 smart00707 RPEL Repeat in Dros 46.1 15 0.00032 19.1 1.3 13 15-27 6-18 (26)
4 PF07960 CBP4: CBP4; InterPro 44.0 13 0.00027 27.0 1.1 12 18-29 29-40 (128)
5 cd00490 Met_repressor_MetJ Met 39.3 37 0.00079 23.1 2.7 38 19-60 50-87 (103)
6 PF12375 DUF3653: Phage protei 39.3 19 0.00042 23.5 1.4 26 2-27 1-26 (76)
7 PF13822 ACC_epsilon: Acyl-CoA 38.5 17 0.00036 22.8 1.0 10 18-27 9-18 (62)
8 COG3060 MetJ Transcriptional r 37.4 20 0.00043 24.2 1.2 39 19-61 51-89 (105)
9 PRK05264 transcriptional repre 35.6 41 0.00089 23.0 2.5 38 19-60 51-88 (105)
10 smart00265 BH4 BH4 Bcl-2 homol 34.7 54 0.0012 17.2 2.4 20 20-39 3-22 (27)
11 PF01473 CW_binding_1: Putativ 34.5 27 0.00058 16.2 1.1 8 65-72 7-14 (19)
12 PLN02417 dihydrodipicolinate s 32.6 31 0.00067 27.8 1.9 18 12-30 103-120 (280)
13 PF01340 MetJ: Met Apo-repress 30.9 47 0.001 22.6 2.2 38 19-60 50-87 (104)
14 cd00952 CHBPH_aldolase Trans-o 29.4 38 0.00081 27.8 1.9 19 10-29 108-126 (309)
15 TIGR02313 HpaI-NOT-DapA 2,4-di 29.3 40 0.00086 27.4 2.0 20 11-31 101-120 (294)
16 cd00954 NAL N-Acetylneuraminic 29.0 44 0.00095 27.0 2.2 19 12-31 103-121 (288)
17 PF08847 DUF1817: Domain of un 26.9 39 0.00085 25.1 1.4 22 10-34 92-113 (150)
18 PF02180 BH4: Bcl-2 homology r 26.3 73 0.0016 16.7 2.0 17 21-37 4-20 (27)
19 PF02755 RPEL: RPEL repeat; I 25.9 41 0.00089 17.4 1.0 11 17-27 8-18 (26)
20 TIGR00674 dapA dihydrodipicoli 24.7 61 0.0013 26.1 2.3 19 12-31 100-118 (285)
21 cd00950 DHDPS Dihydrodipicolin 24.7 53 0.0011 26.2 1.9 19 11-30 101-119 (284)
22 PRK04147 N-acetylneuraminate l 24.2 54 0.0012 26.5 1.9 17 14-30 107-123 (293)
23 PRK03170 dihydrodipicolinate s 23.8 59 0.0013 26.2 2.0 17 12-29 103-119 (292)
24 PF02375 JmjN: jmjN domain; I 23.6 39 0.00085 18.6 0.7 11 17-27 2-12 (34)
25 PRK02079 pyrroloquinoline quin 21.0 55 0.0012 21.9 1.1 12 8-19 4-15 (88)
26 PF07131 DUF1382: Protein of u 20.5 75 0.0016 19.9 1.5 14 14-27 22-39 (61)
No 1
>PF02365 NAM: No apical meristem (NAM) protein; InterPro: IPR003441 The NAC domain (for Petunia hybrida (Petunia) NAM and for Arabidopsis ATAF1, ATAF2, and CUC2) is an N-terminal module of ~160 amino acids, which is found in proteins of the NAC family of plant-specific transcriptional regulators (no apical meristem (NAM) proteins) []. NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defence. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain (DBD) and a dimerization domain [,]. The NAC domain can be subdivided into five subdomains (A-E). Each subdomain is distinguishable by blocks of heterogeneous amino acids or gaps. While the NAC domains were rich in basic amino acids (R, K and H) as a whole, the distribution of positive and negative amino acids in each subdomain were unequal. Subdomains C and D are rich in basic amino acids but poor in acidic amino acids, while subdomain B contains a high proportion of acidic amino acids. Putative nuclear localization signals (NLS) have been detected in subdomains C and D []. The DBD is contained within a 60 amino acid region located within subdomains D and E []. The overall structure of the NAC domain monomer consists of a very twisted antiparallel beta-sheet, which packs against an N-terminal alpha-helix on one side and one shorter helix on the other side surrounded by a few helical elements. The structure suggests that the NAC domain mediates dimerization through conserved interactions including a salt bridge, and DNA binding through the NAC dimer face rich in positive charges [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1UT4_A 3SWM_B 4DUL_B 3SWP_D 1UT7_B 3ULX_A.
Probab=100.00 E-value=8.2e-43 Score=252.98 Aligned_cols=118 Identities=52% Similarity=1.027 Sum_probs=82.5
Q ss_pred CCCCceecCCHHHHHHHHHHHHHcCCCCCC-CeeEeccCCCCCCCCCCccccCCceEEEEEcccCCCCCCCCCCcccCcc
Q 040747 12 LPPCFRFSPTDEELLVLFLRRKVAGRRLSI-NFITEIDFYKFEPWELPSKALFGDYEWFFFSPMDRKNPEASEPNRVTGV 90 (157)
Q Consensus 12 lP~G~rF~PtDeELi~~yL~~k~~g~~~~~-~~I~~~Dvy~~~P~~Lp~~~~~~~~~wyFF~~~~~k~~~g~R~~r~~~~ 90 (157)
|||||||+|||+|||.+||++|+.|.+++. ++|+++|||++|||+|+.....++++||||+++++++.++.|.+|++++
T Consensus 1 LP~G~rF~PtD~ELi~~yL~~k~~g~~~~~~~~i~~~Diy~~~P~~L~~~~~~~~~~~yFF~~~~~~~~~~~r~~R~~~~ 80 (129)
T PF02365_consen 1 LPPGFRFRPTDEELINHYLRPKILGEPLPCEDVIHDVDIYSAHPWELPAKFKGGDEEWYFFSPRKKKYPNGGRPNRVTGG 80 (129)
T ss_dssp --TTEEE---HHHHHHCTHHHHHTT-HHCS-CHSEE--GGGS-GGGCHHHSSS-SSEEEEEEE----------S-EEETT
T ss_pred CCCceEecCChHHHHHHHHHHHhcCCCCCcccceeecccCccChHHhhhhccCCCceEEEEEecccccCCcccccccccc
Confidence 899999999999999999999999999887 7999999999999999954344577999999999999999999999999
Q ss_pred ceeeecCCCCceEEec-CCeEE---------ecCCCCCCCcceEEEEEeeC
Q 040747 91 GYWEDAGSGTDKIITT-AGRKL---------AGNAPNGIKTEWIMHEYRLI 131 (157)
Q Consensus 91 G~Wk~~~~g~~~~i~~-~g~~~---------~g~~~~~~kt~W~M~EY~l~ 131 (157)
|+||. +|+.+.|.. .|..+ .++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~--~g~~~~i~~~~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKS--TGKEKPIKDPGGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEE--ECEEEEEEE-TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEee--cccccccccccceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 99999 777766665 55433 45677889999999999983
No 2
>PHA00692 hypothetical protein
Probab=53.09 E-value=5.1 Score=25.10 Aligned_cols=12 Identities=42% Similarity=0.999 Sum_probs=9.5
Q ss_pred CCCCCCCceecC
Q 040747 9 LISLPPCFRFSP 20 (157)
Q Consensus 9 ~~~lP~G~rF~P 20 (157)
.+..||||||--
T Consensus 34 fveyppgfrfgg 45 (74)
T PHA00692 34 FVEYPPGFRFGG 45 (74)
T ss_pred eEecCCCccccc
Confidence 467899999953
No 3
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=46.12 E-value=15 Score=19.15 Aligned_cols=13 Identities=38% Similarity=0.322 Sum_probs=10.8
Q ss_pred CceecCCHHHHHH
Q 040747 15 CFRFSPTDEELLV 27 (157)
Q Consensus 15 G~rF~PtDeELi~ 27 (157)
...++||.+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3568999999986
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=44.02 E-value=13 Score=27.02 Aligned_cols=12 Identities=42% Similarity=0.736 Sum_probs=10.0
Q ss_pred ecCCHHHHHHHH
Q 040747 18 FSPTDEELLVLF 29 (157)
Q Consensus 18 F~PtDeELi~~y 29 (157)
=.||||||+..|
T Consensus 29 ~tPTeEeL~~r~ 40 (128)
T PF07960_consen 29 TTPTEEELFKRY 40 (128)
T ss_pred cCCCHHHHHHhc
Confidence 379999999865
No 5
>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=39.30 E-value=37 Score=23.09 Aligned_cols=38 Identities=26% Similarity=0.313 Sum_probs=31.2
Q ss_pred cCCHHHHHHHHHHHHHcCCCCCCCeeEeccCCCCCCCCCCcc
Q 040747 19 SPTDEELLVLFLRRKVAGRRLSINFITEIDFYKFEPWELPSK 60 (157)
Q Consensus 19 ~PtDeELi~~yL~~k~~g~~~~~~~I~~~Dvy~~~P~~Lp~~ 60 (157)
|-|-.||++.-...-..|+|+|. +.|+-...|.+||+.
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHH
Confidence 45778999888888899999986 457888889999875
No 6
>PF12375 DUF3653: Phage protein; InterPro: IPR021077 This entry represents a phage protein found in bacteria and viruses, they are typically between 112 and 194 amino acids in length. Note that many members are hypothetical proteins.
Probab=39.28 E-value=19 Score=23.54 Aligned_cols=26 Identities=35% Similarity=0.395 Sum_probs=22.2
Q ss_pred CCccCCCCCCCCCCceecCCHHHHHH
Q 040747 2 GDVFDHDLISLPPCFRFSPTDEELLV 27 (157)
Q Consensus 2 ~~~~~~~~~~lP~G~rF~PtDeELi~ 27 (157)
|+.+....+-.|.|.+|.|.|.+-..
T Consensus 1 Gfr~~~~~LiTPeGr~~~p~~l~~~~ 26 (76)
T PF12375_consen 1 GFRFQGGRLITPEGRRFSPQDLEWWS 26 (76)
T ss_pred CceeeCCeEECCCCCccCHHHHHHHH
Confidence 67778888899999999999987665
No 7
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=38.49 E-value=17 Score=22.76 Aligned_cols=10 Identities=60% Similarity=0.687 Sum_probs=8.2
Q ss_pred ecCCHHHHHH
Q 040747 18 FSPTDEELLV 27 (157)
Q Consensus 18 F~PtDeELi~ 27 (157)
=+||||||--
T Consensus 9 GnPt~eElAA 18 (62)
T PF13822_consen 9 GNPTDEELAA 18 (62)
T ss_pred CCCCHHHHHH
Confidence 3899999865
No 8
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=37.41 E-value=20 Score=24.17 Aligned_cols=39 Identities=28% Similarity=0.353 Sum_probs=31.4
Q ss_pred cCCHHHHHHHHHHHHHcCCCCCCCeeEeccCCCCCCCCCCccc
Q 040747 19 SPTDEELLVLFLRRKVAGRRLSINFITEIDFYKFEPWELPSKA 61 (157)
Q Consensus 19 ~PtDeELi~~yL~~k~~g~~~~~~~I~~~Dvy~~~P~~Lp~~~ 61 (157)
+-|..||++.-...-..|+|+|. +.|+-..-|.+||+.+
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~a 89 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEAA 89 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHHH
Confidence 45778898888888889999985 5688888888998754
No 9
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=35.57 E-value=41 Score=23.00 Aligned_cols=38 Identities=26% Similarity=0.296 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHHHHHcCCCCCCCeeEeccCCCCCCCCCCcc
Q 040747 19 SPTDEELLVLFLRRKVAGRRLSINFITEIDFYKFEPWELPSK 60 (157)
Q Consensus 19 ~PtDeELi~~yL~~k~~g~~~~~~~I~~~Dvy~~~P~~Lp~~ 60 (157)
|-|-.||++.-...-..|+|+|. +-|+-...|.++|+.
T Consensus 51 HATNSELLCEAFLHA~TGQPLP~----D~Dl~Kd~~d~ip~~ 88 (105)
T PRK05264 51 HATNSELLCEAFLHAFTGQPLPD----DEDLRKERSDEIPEA 88 (105)
T ss_pred hcccHHHHHHHHHHHHcCCCCCC----hhhhhhcCcccchHH
Confidence 45778999988888899999986 457888889999864
No 10
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=34.72 E-value=54 Score=17.19 Aligned_cols=20 Identities=20% Similarity=0.308 Sum_probs=15.4
Q ss_pred CCHHHHHHHHHHHHHcCCCC
Q 040747 20 PTDEELLVLFLRRKVAGRRL 39 (157)
Q Consensus 20 PtDeELi~~yL~~k~~g~~~ 39 (157)
.+-.|||.+|+.-|+.-...
T Consensus 3 ~~nRelV~~yv~yKLsQrgy 22 (27)
T smart00265 3 LDNRELVVDYVTYKLSQNGY 22 (27)
T ss_pred cchHHHHHHHHHHHHhhcCC
Confidence 35679999999999875433
No 11
>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=34.52 E-value=27 Score=16.23 Aligned_cols=8 Identities=25% Similarity=1.290 Sum_probs=6.4
Q ss_pred ceEEEEEc
Q 040747 65 DYEWFFFS 72 (157)
Q Consensus 65 ~~~wyFF~ 72 (157)
++.||||.
T Consensus 7 ~~~wYy~~ 14 (19)
T PF01473_consen 7 NGNWYYFD 14 (19)
T ss_dssp TTEEEEET
T ss_pred CCEEEEeC
Confidence 57899995
No 12
>PLN02417 dihydrodipicolinate synthase
Probab=32.56 E-value=31 Score=27.80 Aligned_cols=18 Identities=22% Similarity=0.379 Sum_probs=14.4
Q ss_pred CCCCceecCCHHHHHHHHH
Q 040747 12 LPPCFRFSPTDEELLVLFL 30 (157)
Q Consensus 12 lP~G~rF~PtDeELi~~yL 30 (157)
+|| +.|.||++||+.||-
T Consensus 103 ~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 103 INP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred cCC-ccCCCCHHHHHHHHH
Confidence 555 568999999999774
No 13
>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=30.89 E-value=47 Score=22.62 Aligned_cols=38 Identities=29% Similarity=0.394 Sum_probs=24.6
Q ss_pred cCCHHHHHHHHHHHHHcCCCCCCCeeEeccCCCCCCCCCCcc
Q 040747 19 SPTDEELLVLFLRRKVAGRRLSINFITEIDFYKFEPWELPSK 60 (157)
Q Consensus 19 ~PtDeELi~~yL~~k~~g~~~~~~~I~~~Dvy~~~P~~Lp~~ 60 (157)
|-|..||++.-...-..|+|+|. +.|+-...|.++|..
T Consensus 50 HATNSeLLcEAFLHAfTGQPLP~----D~dl~kd~~d~ip~~ 87 (104)
T PF01340_consen 50 HATNSELLCEAFLHAFTGQPLPT----DDDLRKDRPDEIPAE 87 (104)
T ss_dssp S-SHHHHHHHHHHHHHH----------TTGGGSTSGSSS-HH
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCCccchHH
Confidence 46888999988888899999986 457888899999874
No 14
>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=29.38 E-value=38 Score=27.80 Aligned_cols=19 Identities=5% Similarity=0.155 Sum_probs=14.8
Q ss_pred CCCCCCceecCCHHHHHHHH
Q 040747 10 ISLPPCFRFSPTDEELLVLF 29 (157)
Q Consensus 10 ~~lP~G~rF~PtDeELi~~y 29 (157)
+-+|| |.|.||+++|+.||
T Consensus 108 lv~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 108 MLGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred EECCC-cCCCCCHHHHHHHH
Confidence 34566 56899999999977
No 15
>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=29.29 E-value=40 Score=27.42 Aligned_cols=20 Identities=25% Similarity=0.340 Sum_probs=14.7
Q ss_pred CCCCCceecCCHHHHHHHHHH
Q 040747 11 SLPPCFRFSPTDEELLVLFLR 31 (157)
Q Consensus 11 ~lP~G~rF~PtDeELi~~yL~ 31 (157)
-+||- .|.|++++|+.||-.
T Consensus 101 v~pP~-y~~~~~~~l~~~f~~ 120 (294)
T TIGR02313 101 VIVPY-YNKPNQEALYDHFAE 120 (294)
T ss_pred EcCcc-CCCCCHHHHHHHHHH
Confidence 34554 489999999997743
No 16
>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=29.04 E-value=44 Score=26.96 Aligned_cols=19 Identities=16% Similarity=0.258 Sum_probs=14.0
Q ss_pred CCCCceecCCHHHHHHHHHH
Q 040747 12 LPPCFRFSPTDEELLVLFLR 31 (157)
Q Consensus 12 lP~G~rF~PtDeELi~~yL~ 31 (157)
+||- .|.||++||+.||..
T Consensus 103 ~~P~-y~~~~~~~i~~~~~~ 121 (288)
T cd00954 103 ITPF-YYKFSFEEIKDYYRE 121 (288)
T ss_pred eCCC-CCCCCHHHHHHHHHH
Confidence 4553 478999999997654
No 17
>PF08847 DUF1817: Domain of unknown function (DUF1817); InterPro: IPR014946 Members of this entry are functionally uncharacterised.
Probab=26.93 E-value=39 Score=25.11 Aligned_cols=22 Identities=27% Similarity=0.483 Sum_probs=15.2
Q ss_pred CCCCCCceecCCHHHHHHHHHHHHH
Q 040747 10 ISLPPCFRFSPTDEELLVLFLRRKV 34 (157)
Q Consensus 10 ~~lP~G~rF~PtDeELi~~yL~~k~ 34 (157)
+.--.|++|+|-+.|| |+..|+
T Consensus 92 fs~~eGi~fnPEALEi---fvm~kl 113 (150)
T PF08847_consen 92 FSRKEGIQFNPEALEI---FVMHKL 113 (150)
T ss_pred cccccCceeCHHHHHH---HHHHHH
Confidence 3445699999998888 344444
No 18
>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=26.33 E-value=73 Score=16.72 Aligned_cols=17 Identities=24% Similarity=0.428 Sum_probs=13.3
Q ss_pred CHHHHHHHHHHHHHcCC
Q 040747 21 TDEELLVLFLRRKVAGR 37 (157)
Q Consensus 21 tDeELi~~yL~~k~~g~ 37 (157)
+-.|||.+|+.-|+.-.
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 35799999999888643
No 19
>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=25.95 E-value=41 Score=17.39 Aligned_cols=11 Identities=45% Similarity=0.543 Sum_probs=6.3
Q ss_pred eecCCHHHHHH
Q 040747 17 RFSPTDEELLV 27 (157)
Q Consensus 17 rF~PtDeELi~ 27 (157)
..+|+.+|||.
T Consensus 8 ~~RP~~~eLv~ 18 (26)
T PF02755_consen 8 SQRPTREELVE 18 (26)
T ss_dssp HT---HHHHHH
T ss_pred hcCCCHHHHHH
Confidence 35799999986
No 20
>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=24.71 E-value=61 Score=26.05 Aligned_cols=19 Identities=32% Similarity=0.524 Sum_probs=14.2
Q ss_pred CCCCceecCCHHHHHHHHHH
Q 040747 12 LPPCFRFSPTDEELLVLFLR 31 (157)
Q Consensus 12 lP~G~rF~PtDeELi~~yL~ 31 (157)
+||-| |.||++||+.||..
T Consensus 100 ~pP~y-~~~~~~~i~~~~~~ 118 (285)
T TIGR00674 100 VTPYY-NKPTQEGLYQHFKA 118 (285)
T ss_pred cCCcC-CCCCHHHHHHHHHH
Confidence 45544 78999999997754
No 21
>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=24.68 E-value=53 Score=26.25 Aligned_cols=19 Identities=26% Similarity=0.406 Sum_probs=13.9
Q ss_pred CCCCCceecCCHHHHHHHHH
Q 040747 11 SLPPCFRFSPTDEELLVLFL 30 (157)
Q Consensus 11 ~lP~G~rF~PtDeELi~~yL 30 (157)
-+||. .|.||++||+.||-
T Consensus 101 ~~~P~-~~~~~~~~l~~~~~ 119 (284)
T cd00950 101 VVTPY-YNKPSQEGLYAHFK 119 (284)
T ss_pred Ecccc-cCCCCHHHHHHHHH
Confidence 35664 48899999998553
No 22
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=24.24 E-value=54 Score=26.51 Aligned_cols=17 Identities=18% Similarity=0.186 Sum_probs=12.8
Q ss_pred CCceecCCHHHHHHHHH
Q 040747 14 PCFRFSPTDEELLVLFL 30 (157)
Q Consensus 14 ~G~rF~PtDeELi~~yL 30 (157)
|-+.|.||+++|+.||-
T Consensus 107 ~P~y~~~~~~~l~~~f~ 123 (293)
T PRK04147 107 TPFYYPFSFEEICDYYR 123 (293)
T ss_pred CCcCCCCCHHHHHHHHH
Confidence 33458999999998654
No 23
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=23.75 E-value=59 Score=26.16 Aligned_cols=17 Identities=35% Similarity=0.638 Sum_probs=13.4
Q ss_pred CCCCceecCCHHHHHHHH
Q 040747 12 LPPCFRFSPTDEELLVLF 29 (157)
Q Consensus 12 lP~G~rF~PtDeELi~~y 29 (157)
+||-| |.|+++||+.||
T Consensus 103 ~pP~~-~~~~~~~i~~~~ 119 (292)
T PRK03170 103 VTPYY-NKPTQEGLYQHF 119 (292)
T ss_pred CCCcC-CCCCHHHHHHHH
Confidence 46654 899999999865
No 24
>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=23.62 E-value=39 Score=18.62 Aligned_cols=11 Identities=45% Similarity=0.437 Sum_probs=5.4
Q ss_pred eecCCHHHHHH
Q 040747 17 RFSPTDEELLV 27 (157)
Q Consensus 17 rF~PtDeELi~ 27 (157)
.|+||.||--+
T Consensus 2 vf~Pt~eEF~d 12 (34)
T PF02375_consen 2 VFYPTMEEFKD 12 (34)
T ss_dssp EE---HHHHS-
T ss_pred cccCCHHHHhC
Confidence 48999999754
No 25
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=20.99 E-value=55 Score=21.93 Aligned_cols=12 Identities=33% Similarity=0.758 Sum_probs=9.5
Q ss_pred CCCCCCCCceec
Q 040747 8 DLISLPPCFRFS 19 (157)
Q Consensus 8 ~~~~lP~G~rF~ 19 (157)
+.+.||+||||+
T Consensus 4 ~~p~l~~~~rl~ 15 (88)
T PRK02079 4 QVPTLRPGYRFQ 15 (88)
T ss_pred CCcccCCCcccc
Confidence 457899999987
No 26
>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=20.50 E-value=75 Score=19.92 Aligned_cols=14 Identities=50% Similarity=0.695 Sum_probs=10.5
Q ss_pred CCceecC----CHHHHHH
Q 040747 14 PCFRFSP----TDEELLV 27 (157)
Q Consensus 14 ~G~rF~P----tDeELi~ 27 (157)
.|+||.| ||+|...
T Consensus 22 ~GIRFVpiPv~~dee~~~ 39 (61)
T PF07131_consen 22 IGIRFVPIPVVTDEEFHT 39 (61)
T ss_pred cCceeeccccccHHHHHH
Confidence 5999998 6777643
Done!