Query 031844
Match_columns 152
No_of_seqs 121 out of 871
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 06:08:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031844.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031844hhsearch_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 2E-47 4.3E-52 277.1 6.6 125 14-139 1-129 (129)
2 smart00265 BH4 BH4 Bcl-2 homol 49.5 30 0.00065 18.3 2.8 22 22-43 3-24 (27)
3 PHA00692 hypothetical protein 47.5 7.6 0.00017 24.4 0.4 10 12-21 35-44 (74)
4 cd00490 Met_repressor_MetJ Met 40.6 34 0.00074 23.3 2.7 38 21-62 50-87 (103)
5 PF02180 BH4: Bcl-2 homology r 39.8 45 0.00097 17.6 2.5 21 23-43 4-24 (27)
6 PF07960 CBP4: CBP4; InterPro 38.4 17 0.00038 26.3 1.1 11 21-31 30-40 (128)
7 PRK05264 transcriptional repre 36.5 39 0.00084 23.2 2.5 38 21-62 51-88 (105)
8 PF01340 MetJ: Met Apo-repress 35.9 38 0.00082 23.2 2.4 38 21-62 50-87 (104)
9 PF13822 ACC_epsilon: Acyl-CoA 33.0 23 0.00051 22.1 1.0 9 21-29 10-18 (62)
10 PF08338 DUF1731: Domain of un 31.0 38 0.00081 20.1 1.6 16 16-31 31-47 (48)
11 COG3060 MetJ Transcriptional r 28.8 38 0.00082 22.9 1.5 38 21-62 51-88 (105)
12 PLN02417 dihydrodipicolinate s 26.7 39 0.00084 27.2 1.5 21 11-32 100-120 (280)
13 smart00707 RPEL Repeat in Dros 26.5 48 0.001 17.3 1.3 13 17-29 6-18 (26)
14 TIGR02313 HpaI-NOT-DapA 2,4-di 26.4 41 0.00089 27.3 1.6 21 11-32 99-119 (294)
15 cd00954 NAL N-Acetylneuraminic 25.8 40 0.00086 27.2 1.4 20 12-32 101-120 (288)
16 cd00952 CHBPH_aldolase Trans-o 24.9 42 0.00092 27.5 1.4 20 11-31 107-126 (309)
17 cd00950 DHDPS Dihydrodipicolin 22.8 53 0.0011 26.2 1.6 25 11-37 99-123 (284)
18 TIGR00674 dapA dihydrodipicoli 21.6 66 0.0014 25.8 1.9 22 11-33 97-118 (285)
19 PF12189 VirE1: Single-strand 21.4 39 0.00084 21.2 0.4 26 17-44 33-58 (62)
20 PRK03170 dihydrodipicolinate s 21.0 62 0.0013 26.0 1.7 20 11-31 100-119 (292)
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=2e-47 Score=277.13 Aligned_cols=125 Identities=57% Similarity=1.143 Sum_probs=95.1
Q ss_pred CCCCeEECCChHHHHHHHHHHhHhcCCCCC-CceeecCCCCCCCCCCCc---ccCcceeeeecccccCCCCCCCcccCCC
Q 031844 14 LPPGFRFHPTDEELVVQYLKRKIFACPLPA-SIIPEVDVCKSDPWDLPG---DVAQERYFFSTREAKYPNGNRSNRATGS 89 (152)
Q Consensus 14 LppG~rF~PtDeELi~~yL~~k~~g~~~~~-~~I~~~Dvy~~~P~~Lp~---~~~~~~yFF~~~~~k~~~~~r~~R~~~~ 89 (152)
|||||||+|||+|||.+||.+|+.|.+++. .+|+++|||++|||+|+. ..+++||||++++.++.++.|.+|++++
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 789999999999999993 3357999999999999999999999999
Q ss_pred ceEeeeCCCceEEeCCCCeEEEEEEEEEEEeCCCCCCCCcCeEEEEEEeC
Q 031844 90 GYWKATGLDKQIATSRGNQIVGMKKTLVFYRGKPPHGSRTDWIMHEYRLV 139 (152)
Q Consensus 90 G~Wk~~g~~k~i~~~~~g~~iG~kk~l~f~~~~~~~~~kt~W~M~EY~l~ 139 (152)
|+||.+|+.++|.+. ++.+||+|++|+||.++.+++.+|+|+||||+|.
T Consensus 81 G~Wk~~g~~~~i~~~-~g~~iG~k~~l~f~~~~~~~~~kt~W~M~EY~L~ 129 (129)
T PF02365_consen 81 GYWKSTGKEKPIKDP-GGKVIGFKKTLVFYSGKSPNGKKTGWVMHEYSLE 129 (129)
T ss_dssp EEEEEECEEEEEEE--TTCEEEEEEEEEEEESSTTS-EEEEEEEEEEEE-
T ss_pred eEEeecccccccccc-cceeeeeEEEEEEEeccCCCCCcCCeEEEEEEeC
Confidence 999999999999874 8999999999999998888889999999999984
No 2
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=49.51 E-value=30 Score=18.25 Aligned_cols=22 Identities=27% Similarity=0.289 Sum_probs=16.8
Q ss_pred CChHHHHHHHHHHhHhcCCCCC
Q 031844 22 PTDEELVVQYLKRKIFACPLPA 43 (152)
Q Consensus 22 PtDeELi~~yL~~k~~g~~~~~ 43 (152)
.+-.|||.+|+.-|+.....++
T Consensus 3 ~~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 3 LDNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred cchHHHHHHHHHHHHhhcCCCC
Confidence 3568999999999997665443
No 3
>PHA00692 hypothetical protein
Probab=47.48 E-value=7.6 Score=24.44 Aligned_cols=10 Identities=60% Similarity=1.374 Sum_probs=8.4
Q ss_pred cCCCCCeEEC
Q 031844 12 LRLPPGFRFH 21 (152)
Q Consensus 12 ~~LppG~rF~ 21 (152)
...||||||-
T Consensus 35 veyppgfrfg 44 (74)
T PHA00692 35 VEYPPGFRFG 44 (74)
T ss_pred EecCCCcccc
Confidence 4689999996
No 4
>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=40.59 E-value=34 Score=23.33 Aligned_cols=38 Identities=26% Similarity=0.469 Sum_probs=28.6
Q ss_pred CCChHHHHHHHHHHhHhcCCCCCCceeecCCCCCCCCCCCcc
Q 031844 21 HPTDEELVVQYLKRKIFACPLPASIIPEVDVCKSDPWDLPGD 62 (152)
Q Consensus 21 ~PtDeELi~~yL~~k~~g~~~~~~~I~~~Dvy~~~P~~Lp~~ 62 (152)
|-|..||+..-...-..|+|||. +.|+-...|.++|..
T Consensus 50 HATNSELLCEAFLHAfTGQPLP~----D~Dl~K~~~d~iP~~ 87 (103)
T cd00490 50 HATNSELLCEAFLHAFTGQPLPD----DADLRKERSDEIPEA 87 (103)
T ss_pred hcccHHHHHHHHHHHhcCCCCCC----hhhhhhcCcccccHH
Confidence 45677777666666678999998 458888888888864
No 5
>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=39.82 E-value=45 Score=17.62 Aligned_cols=21 Identities=24% Similarity=0.245 Sum_probs=16.2
Q ss_pred ChHHHHHHHHHHhHhcCCCCC
Q 031844 23 TDEELVVQYLKRKIFACPLPA 43 (152)
Q Consensus 23 tDeELi~~yL~~k~~g~~~~~ 43 (152)
+-.|||.+|+.-|+.....++
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 357999999999997665544
No 6
>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=38.38 E-value=17 Score=26.34 Aligned_cols=11 Identities=55% Similarity=0.951 Sum_probs=9.2
Q ss_pred CCChHHHHHHH
Q 031844 21 HPTDEELVVQY 31 (152)
Q Consensus 21 ~PtDeELi~~y 31 (152)
.||||||+..|
T Consensus 30 tPTeEeL~~r~ 40 (128)
T PF07960_consen 30 TPTEEELFKRY 40 (128)
T ss_pred CCCHHHHHHhc
Confidence 49999999765
No 7
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=36.53 E-value=39 Score=23.20 Aligned_cols=38 Identities=26% Similarity=0.452 Sum_probs=28.4
Q ss_pred CCChHHHHHHHHHHhHhcCCCCCCceeecCCCCCCCCCCCcc
Q 031844 21 HPTDEELVVQYLKRKIFACPLPASIIPEVDVCKSDPWDLPGD 62 (152)
Q Consensus 21 ~PtDeELi~~yL~~k~~g~~~~~~~I~~~Dvy~~~P~~Lp~~ 62 (152)
|-|..||+..-...-..|+|||. +.|+-...|.++|..
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 45677777665666678999998 457888888888854
No 8
>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=35.94 E-value=38 Score=23.15 Aligned_cols=38 Identities=29% Similarity=0.554 Sum_probs=21.7
Q ss_pred CCChHHHHHHHHHHhHhcCCCCCCceeecCCCCCCCCCCCcc
Q 031844 21 HPTDEELVVQYLKRKIFACPLPASIIPEVDVCKSDPWDLPGD 62 (152)
Q Consensus 21 ~PtDeELi~~yL~~k~~g~~~~~~~I~~~Dvy~~~P~~Lp~~ 62 (152)
|-|..||+..-...-..|+|||. +.|+-...|.++|..
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 45777877666666678999998 457888888888854
No 9
>PF13822 ACC_epsilon: Acyl-CoA carboxylase epsilon subunit
Probab=32.95 E-value=23 Score=22.15 Aligned_cols=9 Identities=67% Similarity=1.014 Sum_probs=7.7
Q ss_pred CCChHHHHH
Q 031844 21 HPTDEELVV 29 (152)
Q Consensus 21 ~PtDeELi~ 29 (152)
+||||||-.
T Consensus 10 nPt~eElAA 18 (62)
T PF13822_consen 10 NPTDEELAA 18 (62)
T ss_pred CCCHHHHHH
Confidence 699999974
No 10
>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=30.96 E-value=38 Score=20.09 Aligned_cols=16 Identities=44% Similarity=0.746 Sum_probs=9.4
Q ss_pred CCeEEC-CChHHHHHHH
Q 031844 16 PGFRFH-PTDEELVVQY 31 (152)
Q Consensus 16 pG~rF~-PtDeELi~~y 31 (152)
-||+|. |+=++.+.+.
T Consensus 31 ~GF~F~~p~l~~AL~~l 47 (48)
T PF08338_consen 31 AGFQFRYPTLEEALRDL 47 (48)
T ss_dssp TT---S-SSHHHHHHH-
T ss_pred CCCcccCCCHHHHHhcc
Confidence 599998 8888877654
No 11
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=28.84 E-value=38 Score=22.94 Aligned_cols=38 Identities=26% Similarity=0.477 Sum_probs=28.1
Q ss_pred CCChHHHHHHHHHHhHhcCCCCCCceeecCCCCCCCCCCCcc
Q 031844 21 HPTDEELVVQYLKRKIFACPLPASIIPEVDVCKSDPWDLPGD 62 (152)
Q Consensus 21 ~PtDeELi~~yL~~k~~g~~~~~~~I~~~Dvy~~~P~~Lp~~ 62 (152)
|-|..||+..-...-..|+|+|. +.|+...-|.++|..
T Consensus 51 hatnsellceaflhaftgqplpt----d~dl~ker~deipe~ 88 (105)
T COG3060 51 HATNSELLCEAFLHAFTGQPLPT----DADLRKERSDEIPEA 88 (105)
T ss_pred hhhhHHHHHHHHHHHHcCCCCCC----cHHHHHhccccchHH
Confidence 45667777665666678999987 568888888888764
No 12
>PLN02417 dihydrodipicolinate synthase
Probab=26.69 E-value=39 Score=27.22 Aligned_cols=21 Identities=19% Similarity=0.431 Sum_probs=15.8
Q ss_pred ccCCCCCeEECCChHHHHHHHH
Q 031844 11 VLRLPPGFRFHPTDEELVVQYL 32 (152)
Q Consensus 11 ~~~LppG~rF~PtDeELi~~yL 32 (152)
.+-.|| +-|.||+++|+.||-
T Consensus 100 v~~~~P-~y~~~~~~~i~~~f~ 120 (280)
T PLN02417 100 ALHINP-YYGKTSQEGLIKHFE 120 (280)
T ss_pred EEEcCC-ccCCCCHHHHHHHHH
Confidence 344666 558999999998774
No 13
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=26.52 E-value=48 Score=17.31 Aligned_cols=13 Identities=38% Similarity=0.409 Sum_probs=10.5
Q ss_pred CeEECCChHHHHH
Q 031844 17 GFRFHPTDEELVV 29 (152)
Q Consensus 17 G~rF~PtDeELi~ 29 (152)
....+|+-+|||.
T Consensus 6 kl~~RP~~eeLv~ 18 (26)
T smart00707 6 KLSQRPTREELEE 18 (26)
T ss_pred HHHcCCCHHHHHH
Confidence 3457899999996
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=26.37 E-value=41 Score=27.31 Aligned_cols=21 Identities=19% Similarity=0.411 Sum_probs=15.7
Q ss_pred ccCCCCCeEECCChHHHHHHHH
Q 031844 11 VLRLPPGFRFHPTDEELVVQYL 32 (152)
Q Consensus 11 ~~~LppG~rF~PtDeELi~~yL 32 (152)
.+-+||-| |.|++++|+.||-
T Consensus 99 v~v~pP~y-~~~~~~~l~~~f~ 119 (294)
T TIGR02313 99 AMVIVPYY-NKPNQEALYDHFA 119 (294)
T ss_pred EEEcCccC-CCCCHHHHHHHHH
Confidence 44566655 8999999998764
No 15
>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=25.82 E-value=40 Score=27.17 Aligned_cols=20 Identities=20% Similarity=0.266 Sum_probs=14.6
Q ss_pred cCCCCCeEECCChHHHHHHHH
Q 031844 12 LRLPPGFRFHPTDEELVVQYL 32 (152)
Q Consensus 12 ~~LppG~rF~PtDeELi~~yL 32 (152)
+-+||-| |.||++||+.||.
T Consensus 101 ~~~~P~y-~~~~~~~i~~~~~ 120 (288)
T cd00954 101 SAITPFY-YKFSFEEIKDYYR 120 (288)
T ss_pred EEeCCCC-CCCCHHHHHHHHH
Confidence 3456654 7899999998664
No 16
>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=24.92 E-value=42 Score=27.46 Aligned_cols=20 Identities=15% Similarity=0.121 Sum_probs=15.9
Q ss_pred ccCCCCCeEECCChHHHHHHH
Q 031844 11 VLRLPPGFRFHPTDEELVVQY 31 (152)
Q Consensus 11 ~~~LppG~rF~PtDeELi~~y 31 (152)
.+-+|| |.|.||+++|+.||
T Consensus 107 vlv~~P-~y~~~~~~~l~~yf 126 (309)
T cd00952 107 TMLGRP-MWLPLDVDTAVQFY 126 (309)
T ss_pred EEECCC-cCCCCCHHHHHHHH
Confidence 456777 56889999999876
No 17
>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=22.77 E-value=53 Score=26.22 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=16.9
Q ss_pred ccCCCCCeEECCChHHHHHHHHHHhHh
Q 031844 11 VLRLPPGFRFHPTDEELVVQYLKRKIF 37 (152)
Q Consensus 11 ~~~LppG~rF~PtDeELi~~yL~~k~~ 37 (152)
.+-+||.| |.||+++|+.|| +.-+.
T Consensus 99 v~~~~P~~-~~~~~~~l~~~~-~~ia~ 123 (284)
T cd00950 99 ALVVTPYY-NKPSQEGLYAHF-KAIAE 123 (284)
T ss_pred EEEccccc-CCCCHHHHHHHH-HHHHh
Confidence 45567755 889999999754 44333
No 18
>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=21.58 E-value=66 Score=25.82 Aligned_cols=22 Identities=27% Similarity=0.443 Sum_probs=16.1
Q ss_pred ccCCCCCeEECCChHHHHHHHHH
Q 031844 11 VLRLPPGFRFHPTDEELVVQYLK 33 (152)
Q Consensus 11 ~~~LppG~rF~PtDeELi~~yL~ 33 (152)
.+-+||-| |.||+++|+.||..
T Consensus 97 v~v~pP~y-~~~~~~~i~~~~~~ 118 (285)
T TIGR00674 97 FLVVTPYY-NKPTQEGLYQHFKA 118 (285)
T ss_pred EEEcCCcC-CCCCHHHHHHHHHH
Confidence 44566665 78999999987653
No 19
>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=21.42 E-value=39 Score=21.21 Aligned_cols=26 Identities=31% Similarity=0.609 Sum_probs=16.0
Q ss_pred CeEECCChHHHHHHHHHHhHhcCCCCCC
Q 031844 17 GFRFHPTDEELVVQYLKRKIFACPLPAS 44 (152)
Q Consensus 17 G~rF~PtDeELi~~yL~~k~~g~~~~~~ 44 (152)
-..|.|-|-++|+ |-..+...|+|.+
T Consensus 33 ~~gFtslDL~mIE--LE~Fvl~cPlP~~ 58 (62)
T PF12189_consen 33 PNGFTSLDLEMIE--LENFVLRCPLPED 58 (62)
T ss_dssp TTTS-HHHHHHHH--HHHHHHT------
T ss_pred CCCcccccHHHHH--HHHHHHhCCCCcc
Confidence 3458899999997 8999999998864
No 20
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=21.02 E-value=62 Score=25.99 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=15.0
Q ss_pred ccCCCCCeEECCChHHHHHHH
Q 031844 11 VLRLPPGFRFHPTDEELVVQY 31 (152)
Q Consensus 11 ~~~LppG~rF~PtDeELi~~y 31 (152)
.+-+||-| |.|++++|+.||
T Consensus 100 v~~~pP~~-~~~~~~~i~~~~ 119 (292)
T PRK03170 100 ALVVTPYY-NKPTQEGLYQHF 119 (292)
T ss_pred EEECCCcC-CCCCHHHHHHHH
Confidence 44567765 889999999765
Done!