name | startcoord | endcoord | * | * | de | intron | start1 | direction | status | gn | ec | gp | cc | type1 | kognum | kog | glimmer | dompat | auth | 10/10/03 00:00:00 | More Comments | |
LUAcid_KM3_F8_01 | 105 | 296 | | | hypothetical protein | | 1 | D | ADDED | | | | no matches | PROTEIN | | | - | | 82.227.62.180 | 13/09/07 18:10:54 | | |
LUAcid_KM3_F8_02 | 420 | 1271 | | | dihydropteroate synthase | | 1 | D | ADDED | | | | - 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 morismortii | PROTEIN | COG0294 Dihydropteroate synthase and related enzymes | H Coenzyme transport and metabolism | Good | | 82.227.62.180 | 13/09/07 18:18:37 | | |
LUAcid_KM3_F8_03 | 1341 | 2714 | | | phosphoglucosamine mutase | | 1 | D | ADDED | | | | - 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. | PROTEIN | COG1109 Phosphomannomutase | G Carbohydrate transport and metabolism | Good | | 82.227.62.180 | 13/09/07 18:26:53 | | |
LUAcid_KM3_F8_04 | 8299 | 9099 | | | conserved hypothetical protein | | 1 | D | ADDED | | | | - conserved only in Acidobacteria 43% and 54% identities - present in both sequenced genome - no other significant matches - no domains | PROTEIN | | | Good | | 82.227.62.180 | 13/09/07 18:32:47 | | |
LUAcid_KM3_F8_05 | 10596 | 9130 | | | leucyl aminopeptidase | | 1 | R | ADDED | | | | - present in both sequenced Acidobacteria - peptidase M17 domain - not present in other acidobacterial clones - conserved in bacteria and some A and E | PROTEIN | COG0260 Leucyl aminopeptidase | E Amino acid transport and metabolism | Good | | 82.227.62.180 | 13/09/07 19:04:15 | | |
LUAcid_KM3_F8_06 | 12692 | 10968 | | | peptidase S15; hydrolase CocE/nonD family | | 1 | R | ADDED | | | | - three matches in both acidobacteria whole genome sequences, but not paralogs - very large family - not in clone sequences - peptidase S15 domain | PROTEIN | COG2936 Predicted acyl esterases | R General function prediction only | Good | | 82.227.62.180 | 13/09/07 19:10:19 | | |
LUAcid_KM3_F8_07 | 13142 | 16303 | | | conserved hypothetical protein | | 1 | D | ADDED | | | | - 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 domain | PROTEIN | | | Good | | 82.227.62.180 | 13/09/07 20:56:16 | | |
LUAcid_KM3_F8_08 | 16281 | 17753 | | | protein of unknown function DUF1501 | | 1 | D | ADDED | | | | 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 compartimentalisation | PROTEIN | | | Good | | 82.227.62.180 | 13/09/07 21:08:48 | | |
LUAcid_KM3_F8_09 | 18004 | 19086 | | | beta-lactamase domain protein | | 1 | D | ADDED | | | | - 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 proteins | PROTEIN | COG2333 Predicted hydrolase (metallo-beta-lactamase superfamily) | R General function prediction only | Good | | 82.227.62.180 | 14/09/07 05:42:00 | | |
LUAcid_KM3_F8_10 | 20355 | 19126 | | | Mandelate racemase/muconate lactonizing enzyme-like | | 1 | R | ADDED | | | | - 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 clones | PROTEIN | COG4948 L-alanine-DL-glutamate epimerase and related enzymes of enolase superfamily | M Cell wall/membrane/envelope biogenesis | Good | | 82.227.62.180 | 14/09/07 05:55:10 | | |
LUAcid_KM3_F8_11 | 21855 | 20374 | | | protein of unknown function DUF1501 | | 1 | R | ADDED | | | | - 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 116 | PROTEIN | | | Good | | 82.227.62.180 | 14/09/07 06:03:48 | | |
LUAcid_KM3_F8_12 | 24942 | 21871 | | | protein of unknown function DUF1549 | | 1 | R | ADDED | | | | - 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 C | PROTEIN | | | Good | | 82.227.62.180 | 14/09/07 06:17:56 | | |
LUAcid_KM3_F8_13 | 25029 | 26132 | | | hypthetical protein | | 1 | D | ADDED | | | | - 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 conserved | PROTEIN | | | Good | | 82.227.62.180 | 14/09/07 06:27:58 | | |
LUAcid_KM3_F8_14 | 27493 | 26150 | | | hypothetical protein | | 1 | R | ADDED | | | | - best but low match to Schizosaccharomyces bombe - unique protein for this clone - not in other clones | PROTEIN | | | Good | | 82.227.62.180 | 14/09/07 06:30:28 | | |
LUAcid_KM3_F8_15 | 28306 | 27551 | | | short-chain dehydrogenase/reductase SDR | | 1 | R | ADDED | | | | - 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 | PROTEIN | COG1028 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) | I Lipid transport and metabolism | Good | | 82.227.62.180 | 14/09/07 06:57:14 | | |
LUAcid_KM3_F8_17 | 31010 | 29655 | | | Fe-S oxidoreductase, related to NifB/MoaA family | | 1 | R | ADDED | | | | - 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 domain | PROTEIN | COG1625 Fe-S oxidoreductase, related to NifB/MoaA family | C Energy production and conversion | Good | | 82.227.62.180 | 14/09/07 09:56:50 | | |
LUAcid_KM3_F8_18 | 31614 | 31042 | | | phosphatidylglycerophosphate synthase | | 1 | R | ADDED | | | | - 39% identity to Acid345_3995 (Ellin345) - conserved in Bacteria not A and E - two matches in each Solibacter and Ellin345 - not in acidobacterial clones | PROTEIN | COG0558 Phosphatidylglycerophosphate synthase | I Lipid transport and metabolism | Good | | 82.227.62.180 | 14/09/07 10:01:58 | | |
LUAcid_KM3_F8_19 | 32356 | 32003 | | | hypothetical protein (DUF454) | | 1 | R | ADDED | | | | - best hit to Maricaulis maris MCS10 (39% identity) - conserved only in proteobacteria - no hits to other clones and acidobacterial sequence | PROTEIN | | | - | | 82.227.62.180 | 14/09/07 10:20:57 | | |
LUAcid_KM3_F8_20 | 33978 | 32494 | | | transporter, solute:sodium symporter (SSS) family protein | | 1 | R | ADDED | | | | - 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) | PROTEIN | COG0591 Na+/proline symporter | E Amino acid transport and metabolism | Good | | 82.227.62.180 | 14/09/07 10:26:35 | | |
LUAcid_KM3_F8_21 | 35379 | 34051 | | | glutamate-1-semialdehyde-2,1-aminomutase | | 1 | R | ADDED | | | | - 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 COG0161 | PROTEIN | COG0001 Glutamate-1-semialdehyde aminotransferase | H Coenzyme transport and metabolism | Good | | 82.227.62.180 | 14/09/07 10:32:57 | | |
LUAcid_KM3_F8_22 | 36405 | 35437 | | | porphobilinogen synthase | | 1 | R | ADDED | | | | - 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] | PROTEIN | COG0113 Delta-aminolevulinic acid dehydratase | H Coenzyme transport and metabolism | Good | | 82.227.62.180 | 14/09/07 10:43:54 | | |
LUAcid_KM3_F8_23 | 36802 | 38496 | | | ASPIC/UnbV domain protein | | 1 | D | ADDED | | | | - 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 | | 82.227.62.180 | 14/09/07 10:47:43 | | |
LUAcid_KM3_F8_24 | 38578 | 39573 | | | Tetratricopeptide TPR_2 repeat protein | | 1 | D | ADDED | | | | - best match to Candidatus Kuenenia stuttgartiensis (26% identity) - similar to N-acetylglucosaminyltransferases - no matches on acidobacterial clones | PROTEIN | COG0457 FOG: TPR repeat | R General function prediction only | Good | | 82.227.62.180 | 14/09/07 10:51:22 | | |
LUAcid_KM3_F8_16 | 29299 | 28460 | | | transmembrane, protein of unknown function DUF6 | | 1 | R | ADDED | | | | - 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 regulation | PROTEIN | COG0697 Permeases of the drug/metabolite transporter (DMT) superfamily | G Carbohydrate transport and metabolism | Good | ABE | 82.227.62.180 | 19/09/07 11:22:50 | - no matches to Acidobacteria | |
LUAcid_KM3_F8_25 | 40124 | 39636 | | | partial dioxygenase | | 1 | R | ADDED | | | | - 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 domain | PROTEIN | | | Good but overlapping | ABE | 82.227.62.180 | 21/09/07 08:51:55 | - low match in Acid_3663 | |
LUAcid_KM3_F8_26 | 40386 | 39973 | | | partial dioxygenase (N-terminal) | | 17 | R | ADDED | | | | - 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 domain | PROTEIN | | | Good but overlapping | BE | 82.227.62.180 | 21/09/07 09:00:05 | - no match in Acidobacteria | |
LUAcid_KM3_F8_27 | 41078 | 40434 | | | hypothetical protein | | 1 | R | ADDED | | | | - no match - no COG - no other match at the end of the fragment after blastx and ORF finder | PROTEIN | | | Good | unique | 82.227.62.180 | 21/09/07 09:01:36 | | |
LUACID_KM3_F8_03 | 1341 | 2714 | | | phosphoglucosamine mutase | | 1 | D | ADDED | | 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. | PROTEIN | COG1109 Phosphomannomutase | G Carbohydrate transport and metabolism | Good | | 82.227.62.180 | 17/10/07 06:17:56 | | |
LUACID_KM3_F8_16SRNA | 3031 | 4558 | | | 16S ribosomal RNA | | 1 | D | ADDED | 16SrRNA | | | | RNA | | | - | | 129.175.105.75 | 29/10/07 17:43:39 | | |
LUACID_KM3_F8_23SRNA | 5079 | 7923 | | | 23S ribosomal RNA | | 1 | D | ADDED | 23SrRNA | | | | RNA | | | | | 129.175.105.75 | 29/10/07 17:44:08 | | |
LUACID_KM3_F8_5SRNA | 8104 | 8211 | | | 5S ribosomal RNA | | 1 | D | ADDED | 5SrRNA | | | | RNA | | | | | 129.175.105.75 | 29/10/07 17:44:27 | | |
LUACID_KM3_F8_TRNA1 | 4721 | 4794 | | | tRNA-Ile (GAT) | | 1 | D | ADDED | tRNA-Ile | | | | TRNA | | | | | 129.175.105.75 | 29/10/07 17:45:39 | | |
LUACID_KM3_F8_TRNA2 | 4878 | 4950 | | | tRNA-Ala (TGC) | | 1 | D | ADDED | tRNA-Ala | | | | TRNA | | | | | 129.175.105.75 | 29/10/07 17:46:18 | | |
LUACID_KM3_F8_TRNA3 | 31855 | 31784 | | | tRNA-Val (CAC) | | 1 | R | ADDED | tRNA-Val | | | | TRNA | | | | | 129.175.105.75 | 29/10/07 17:47:39 | | |
LUACID_KM3_F8_07 | 13142 | 16303 | | | secreted protein of unknown function DUF1549 | | 1 | D | ADDED | | | | - 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 domain | PROTEIN | | | Good | | 82.227.62.180 | 13/12/07 09:35:25 | | |
LUACID_KM3_F8_12 | 24942 | 21871 | | | secreted protein of unknown function DUF1549 | | 1 | R | ADDED | | | | - 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 C | PROTEIN | | | Good | | 82.227.62.180 | 13/12/07 09:42:24 | |