Current Annotation for L35505_KM3_18_F8 23/11/17

namestartcoordendcoord**deintronstart1directionstatusgnecgpcctype1kognumkogglimmerdompatauth10/10/03 00:00:00More Comments 
LUAcid_KM3_F8_01105296  hypothetical protein 1DADDED   no matchesPROTEIN  - 82.227.62.18013/09/07 18:10:54  
LUAcid_KM3_F8_024201271  dihydropteroate synthase 1DADDED   - best match to Carboxydothermus hydrogenoformans Z-2901, very conserved 47% identity - present on acidobacterial clone from Liles et al, but lower similarity - present in both sequenced acidobacterial genomes - not present on other clones - conserved in Bacteria, in Archaea only in Haloarcula morismortiiPROTEINCOG0294 Dihydropteroate synthase and related enzymesH Coenzyme transport and metabolismGood 82.227.62.18013/09/07 18:18:37  
LUAcid_KM3_F8_0313412714  phosphoglucosamine mutase 1DADDED   - best match to Solibacter and A. bacterium - environment not conserved - Phosphoglucomutase (EC:5.4.2.2) (PGM) is responsible for the conversion of D-glucose 1-phosphate to D-glucose 6-phosphate. The enzyme participates in both the breakdown and synthesis of glucose [1]. Phosphomannomutase (EC:5.4.2.8) (PMM) is involved in the conversion of D-mannose 1-phosphate to D-mannose 6-phosphate [2]. The enzyme is required for different biosynthetic pathways in bacteria.PROTEINCOG1109 PhosphomannomutaseG Carbohydrate transport and metabolismGood 82.227.62.18013/09/07 18:26:53  
LUAcid_KM3_F8_0482999099  conserved hypothetical protein 1DADDED   - conserved only in Acidobacteria 43% and 54% identities - present in both sequenced genome - no other significant matches - no domainsPROTEIN  Good 82.227.62.18013/09/07 18:32:47  
LUAcid_KM3_F8_05105969130  leucyl aminopeptidase 1RADDED   - present in both sequenced Acidobacteria - peptidase M17 domain - not present in other acidobacterial clones - conserved in bacteria and some A and E PROTEINCOG0260 Leucyl aminopeptidaseE Amino acid transport and metabolismGood 82.227.62.18013/09/07 19:04:15  
LUAcid_KM3_F8_061269210968  peptidase S15; hydrolase CocE/nonD family 1RADDED   - three matches in both acidobacteria whole genome sequences, but not paralogs - very large family- nod Ún clone sequences - peptidase S15 domainPROTEINCOG2936 Predicted acyl esterasesR General function prediction onlyGood 82.227.62.18013/09/07 19:10:19  
LUAcid_KM3_F8_071314216303  conserved hypothetical protein 1DADDED   - homologs only in a small number of bacterial groups, Planctomycetes, Bacteroides... also in Poribacteria sponge clone - high number of paralogs in Planctomycetes, Solibacter .... - paralog on clone: KM3_18_F8_187 (ORF187) - often in tandem 2 paralogs as in Probacteria - idea was that it could be involved in cell compartimentalisation - cytochrome C domain - DUF1549 domain: This domain is found in a family of paralogues in the planctomycetes. The function is not known. It is found associated with the Planctomycete cytochrome C domainPROTEIN  Good 82.227.62.18013/09/07 20:56:16  
LUAcid_KM3_F8_081628117753  protein of unknown function DUF1501 1DADDED   bacterial groups, Planctomycetes, Bacteroides... also in Poribacteria sponge clone - high number of paralogs in Plan- paralog on same clone KM3_18_F8_163 (ORF163) - homolog on another acidobacterial deep sea clone: AD370_D1_326 - often in tandem with DUF1549 protein as here ORF128 and 116, same in other microorganisms - paralog on clone: KM3_18_F8_187 (ORF187) - often in tandem 2 paralogs as in Probacteria - idea was that it could be involved in cell compartimentalisationPROTEIN  Good 82.227.62.18013/09/07 21:08:48  
LUAcid_KM3_F8_091800419086  beta-lactamase domain protein 1DADDED   - best matches to 2 paralogs in Solibacter and one in Ellin345, conserved in Acidobacteria 38% identity and corresponding protein length, lower matches in other MO and different length (27% identity) - not present on other clones - beta lactamase domain COG - Metallo-hydrolase/oxidoreductuase Pfam - environment not conserved - low similarity to some A and E proteinsPROTEINCOG2333 Predicted hydrolase (metallo-beta-lactamase superfamily)R General function prediction onlyGood 82.227.62.18014/09/07 05:42:00  
LUAcid_KM3_F8_102035519126  Mandelate racemase/muconate lactonizing enzyme-like 1RADDED   - best match to Mesorhizobium 48% identity - general function prediction only - similarity to high number of matches in Solibacter but only one low match in Ellin345 - no matches in acidobacterial clonesPROTEINCOG4948 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamilyM Cell wall/membrane/envelope biogenesisGood 82.227.62.18014/09/07 05:55:10  
LUAcid_KM3_F8_112185520374  protein of unknown function DUF1501 1RADDED   - high number of paralogs in Plancto, Solibacter...Poribacteria - paralog on same clone KM3_18_F8_128 (ORF128) - homolog on another acidobacterial deep sea clone: AD370_D1_326 - often in tandem with DUF1549 protein as here ORF128 and 116PROTEIN  Good 82.227.62.18014/09/07 06:03:48  
LUAcid_KM3_F8_122494221871  protein of unknown function DUF1549 1RADDED   - conserved in Plancto, Solibacteria, Proibacteria... - conserved in tandem DUF1501 and DUF1549 - two tandems present on this clone: 116+128 and 163+187 - 128 homolog to 163 and 116 to 187 - InterPro: Plancto cytochrome C: These proteins share a region of homology at their N terminus that contains the C-{CPWHF}-{CPWR}-C-H-{CFYW} motif typical of cytochromes CPROTEIN  Good 82.227.62.18014/09/07 06:17:56  
LUAcid_KM3_F8_132502926132  hypthetical protein 1DADDED   - best but low match to Exo-alpha-sialidase (Palnctomyces maris) - interPro: sialidases (neuramiases) domain - no match in other clones - low match in Solibacter (Acid_0193) - environment not conservedPROTEIN  Good 82.227.62.18014/09/07 06:27:58  
LUAcid_KM3_F8_142749326150  hypothetical protein 1RADDED   - best but low match to Schizosaccharomyces bombe - unique protein for this clone - not in other clonesPROTEIN  Good 82.227.62.18014/09/07 06:30:28  
LUAcid_KM3_F8_152830627551  short-chain dehydrogenase/reductase SDR 1RADDED   - conserved in bacteria (48% identity to Blastopirellula), only one match in Archaea (Caldivirga, Cren, thermo) - ortholog on another clone: AD17_E3_146 (31% identity); origin not known? - high number of matches but lower similarity to Solibacter and Ellin345 PROTEINCOG1028 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)I Lipid transport and metabolismGood 82.227.62.18014/09/07 06:57:14  
LUAcid_KM3_F8_173101029655  Fe-S oxidoreductase, related to NifB/MoaA family 1RADDED   - no matches to other acidobacterial clones - PDZ domain (peptide binding domain): PDZ domains are found in diverse signaling proteins in bacteria, yeasts, plants, insects and vertebrates - Radical SAM domain - DUF512 domainPROTEINCOG1625 Fe-S oxidoreductase, related to NifB/MoaA familyC Energy production and conversionGood 82.227.62.18014/09/07 09:56:50  
LUAcid_KM3_F8_183161431042  phosphatidylglycerophosphate synthase 1RADDED   - 39% identity to Acid345_3995 (Ellin345) - conserved in Bacteria not A and E - two matches in each Solibacter and Ellin345 - not in acidobacterial clonesPROTEINCOG0558 Phosphatidylglycerophosphate synthaseI Lipid transport and metabolismGood 82.227.62.18014/09/07 10:01:58  
LUAcid_KM3_F8_193235632003  hypothetical protein (DUF454) 1RADDED   - best hit to Maricaulis maris MCS10 (39% identity) - conserved only in proteobacteria - no hits to other clones and acidobacterial sequencePROTEIN  - 82.227.62.18014/09/07 10:20:57  
LUAcid_KM3_F8_203397832494  transporter, solute:sodium symporter (SSS) family protein 1RADDED   - best match to Salinibacter ruber DSM 13855 (40% identity) - several matches in both sequenced acidobacterial genomes (38% identity) - match to AD370_D1_131 (22% identity)PROTEINCOG0591 Na+/proline symporterE Amino acid transport and metabolismGood 82.227.62.18014/09/07 10:26:35  
LUAcid_KM3_F8_213537934051  glutamate-1-semialdehyde-2,1-aminomutase 1RADDED   - best match to Synechococcus sp. JA-3-3Ab (56% identity) - matches in other clones: AD370_D1_346 (31%) and AD17_E3_320 (23%) - other COGs E COG0160, E COG4992, H COG0161PROTEINCOG0001 Glutamate-1-semialdehyde aminotransferaseH Coenzyme transport and metabolismGood 82.227.62.18014/09/07 10:32:57  
LUAcid_KM3_F8_223640535437  porphobilinogen synthase 1RADDED   - conserved in Bacteria and found in some euryarchaeota - one match in each acidobacterial genome (Solibacter and Ellin345) - Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway [1]. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin [2]PROTEINCOG0113 Delta-aminolevulinic acid dehydrataseH Coenzyme transport and metabolismGood 82.227.62.18014/09/07 10:43:54  
LUAcid_KM3_F8_233680238496  ASPIC/UnbV domain protein 1DADDED   - best match to Ellin345 (43% identity) - no matches in acidobacterial clones - This conserved sequence is found associated with IPR001440 in several paralogous proteins in Rhodopirellula baltica. It is also found associated with IPR000413 in several eukaryotic integrin-like proteins (e.g. human ASPIC Q9NQ78) and in several other bacterial proteins (e.g. Q84HN1) [1]PROTEIN  Good 82.227.62.18014/09/07 10:47:43  
LUAcid_KM3_F8_243857839573  Tetratricopeptide TPR_2 repeat protein 1DADDED   - best match to Candidatus Kuenenia stuttgartiensis (26% identity) - similar to N-acetylglucosaminyltransferases - no matches on acidobacterial clonesPROTEINCOG0457 FOG: TPR repeatR General function prediction onlyGood 82.227.62.18014/09/07 10:51:22  
LUAcid_KM3_F8_162929928460  transmembrane, protein of unknown function DUF6 1RADDED   - best match to integral membrane protein Synechococcus (39% id) - IPR000620 Protein of unknown function DUF6, transmembrane - This domain is found in proteins including the Erwinia chrysanthemi PecM protein, which is involved in pectinase, cellulase and blue pigment regulationPROTEINCOG0697 Permeases of the drug/metabolite transporter (DMT) superfamilyG Carbohydrate transport and metabolismGoodABE82.227.62.18019/09/07 11:22:50- no matches to Acidobacteria 
LUAcid_KM3_F8_254012439636  partial dioxygenase 1RADDED   - partial C-terminal ORF (160aa from 250; lack of 90aa) - frame shift with adjacent ORF - no COG - PR008775 Phytanoyl-CoA : This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins as well as a number of bacterial deoxygenases; dioxygenase domainPROTEIN  Good but overlappingABE82.227.62.18021/09/07 08:51:55- low match in Acid_3663 
LUAcid_KM3_F8_264038639973  partial dioxygenase (N-terminal) 17RADDED   - partial N-terminal ORF (100aa from 250; lack of 150aa C-terminal) - frame shift with adjacent ORF - no COG - PR008775 Phytanoyl-CoA : This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins as well as a number of bacterial deoxygenases; dioxygenase domainPROTEIN  Good but overlappingBE82.227.62.18021/09/07 09:00:05- no match in Acidobacteria 
LUAcid_KM3_F8_274107840434  hypothetical protein 1RADDED   - no match - no COG - no other match at the end of the fragment after blastx and ORF finderPROTEIN  Goodunique82.227.62.18021/09/07 09:01:36  
LUACID_KM3_F8_0313412714  phosphoglucosamine mutase 1DADDED 5.4.2.10 - best match to Solibacter and A. bacterium - environment not conserved - Phosphoglucomutase (EC:5.4.2.2) (PGM) is responsible for the conversion of D-glucose 1-phosphate to D-glucose 6-phosphate. The enzyme participates in both the breakdown and synthesis of glucose [1]. Phosphomannomutase (EC:5.4.2.8) (PMM) is involved in the conversion of D-mannose 1-phosphate to D-mannose 6-phosphate [2]. The enzyme is required for different biosynthetic pathways in bacteria.PROTEINCOG1109 PhosphomannomutaseG Carbohydrate transport and metabolismGood 82.227.62.18017/10/07 06:17:56  
LUACID_KM3_F8_16SRNA30314558  16S ribosomal RNA 1DADDED16SrRNA   RNA  - 129.175.105.7529/10/07 17:43:39  
LUACID_KM3_F8_23SRNA50797923  23S ribosomal RNA 1DADDED23SrRNA   RNA    129.175.105.7529/10/07 17:44:08  
LUACID_KM3_F8_5SRNA81048211  5S ribosomal RNA 1DADDED5SrRNA   RNA    129.175.105.7529/10/07 17:44:27  
LUACID_KM3_F8_TRNA147214794  tRNA-Ile (GAT) 1DADDEDtRNA-Ile   TRNA    129.175.105.7529/10/07 17:45:39  
LUACID_KM3_F8_TRNA248784950  tRNA-Ala (TGC) 1DADDEDtRNA-Ala   TRNA    129.175.105.7529/10/07 17:46:18  
LUACID_KM3_F8_TRNA33185531784  tRNA-Val (CAC) 1RADDEDtRNA-Val   TRNA    129.175.105.7529/10/07 17:47:39  
LUACID_KM3_F8_071314216303  secreted protein of unknown function DUF1549 1DADDED   - homologs only in a small number of bacterial groups, Planctomycetes, Bacteroides... also in Poribacteria sponge clone - high number of paralogs in Planctomycetes, Solibacter .... - paralog on clone: KM3_18_F8_187 (ORF187) - often in tandem 2 paralogs as in Probacteria - idea was that it could be involved in cell compartimentalisation - cytochrome C domain - DUF1549 domain: This domain is found in a family of paralogues in the planctomycetes. The function is not known. It is found associated with the Planctomycete cytochrome C domainPROTEIN  Good 82.227.62.18013/12/07 09:35:25  
LUACID_KM3_F8_122494221871  secreted protein of unknown function DUF1549 1RADDED   - conserved in Plancto, Solibacteria, Proibacteria... - conserved in tandem DUF1501 and DUF1549 - two tandems present on this clone: 116+128 and 163+187 - 128 homolog to 163 and 116 to 187 - InterPro: Plancto cytochrome C: These proteins share a region of homology at their N terminus that contains the C-{CPWHF}-{CPWR}-C-H-{CFYW} motif typical of cytochromes CPROTEIN  Good 82.227.62.18013/12/07 09:42:24