| 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 | |
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| LUAcid_KM4_H7_24 | 20096 | 20770 | | | beta-lactamase-like protein | | 1 | D | ADDED | | | | - protein N-terminal too short (60aa?) - best match euryarchaeote: eta-lactamase domain protein, Candidatus Methanoregula boonei 6A8 (35% id), then bacteria - also COG0324 - seems to be part of purin operon | PROTEIN | COG1235 Metal-dependent hydrolases of the beta-lactamase superfamily I | R General function prediction only | Good | BE | 82.227.62.180 | 18/09/07 10:59:17 | - paralogs on different clones LUAcid_KM3_G1_01 LUAcid_KM3_D9_13 LUAcid_AD106_G4_08 L35498_AD55_D2_360 LUAcid_KM4_H7_24 | |
| LUAcid_KM4_H7_25 | 20844 | 22154 | | | adenylosuccinate lyase (PurB) | | 1 | D | ADDED | | | | - best match to AD55_D2_353 (70% id) - next match 23k22_16 (70% id) - purine ribonucleotide biosynthetic process | PROTEIN | COG0015 Adenylosuccinate lyase | F Nucleotide transport and metabolism | Good | ABE | 82.227.62.180 | 18/09/07 11:33:11 | - orthologs found in other clones: LUAcid_KM3_G1_02 LUAcid_KM3_D9_14 L35498_AD55_D2_353 LUAcid_AD106_G4_09 LUAcid_KM4_H7_25 23k22_016 PurB (AY281356 soil clone) 41b15_012 PurB (AY281352 soil clone) | |
| LUAcid_KM4_H7_26 | 22209 | 22472 | | | phosphoribosylformylglycinamidine synthase I (PurS) | | 1 | D | ADDED | | | | - best match to 23k22_011 PurS soil clone AY281352 (73% id) - purin biosynthesis pathway | PROTEIN | COG1828 Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component | F Nucleotide transport and metabolism | Good | AB | 82.227.62.180 | 18/09/07 11:48:26 | - orthologs on other acidobacterial clones: LUAcid_KM3_G1_03 L35498_AD55_D2_340 LUAcid_KM3_D9_15 LUAcid_AD106_G4_10 LUAcid_KM4_H7_26 23k22_011 PurS AY281352 41b15_015 PurS AY281356 | |
| LUAcid_KM4_H7_27 | 22533 | 23240 | | | phosphoribosylformylglycinamidine synthase I (PurQ) | | 1 | D | ADDED | | | | best match to KM3_205_D9_262 (84% id) - Purin biosynthesis operon | PROTEIN | COG0047 Phosphoribosylformylglycinamidine (FGAM) synthase, glutamine amidotransferase domain | F Nucleotide transport and metabolism | Good | AB | 82.227.62.180 | 18/09/07 13:10:00 | - several orthologs in Acidobacteria LUAcid_KM3_G1_04 LUAcid_KM3_D9_16 L35498_AD55_D2_336 LUAcid_AD106_G4_11 LUAcid_KM4_H7_27 41b15_014 PurQ AY281356 23k22_010 PurQ AY281352 Acid345_2235 Acid_5943 | |
| LUAcid_KM4_H7_28 | 23265 | 25478 | | | phosphoribosylformylglycinamidine synthase II (PurL) | | 1 | D | ADDED | | 6.3.5.3 | | best match to 23k22_009 PurL AY281352 (66% id) - purin biosynthesis operon - AIR synthase related protein - ’de novo’ IMP biosynthetic process - hosphoribosylformylglycinamidine synthase is a single, long polypeptide in most bacteria. Three proteins are required in Bacillus subtilis and many other species. This is the longest of the three and is designated PurL, phosphoribosylformylglycinamidine synthase II, or FGAM synthase II. | PROTEIN | COG0046 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain | F Nucleotide transport and metabolism | Good | AB | 82.227.62.180 | 18/09/07 14:01:29 | several orthologs in Acidobacteria: LUAcid_KM3_G1_06 LUAcid_KM3_D9_17 L35498_AD55_D2_328 LUAcid_AD106_G4_12 LUAcid_KM4_H7_28 L35511_KM3_47_B8_428 23k22_009 PurL AY281352 41b15_013 PurL AY281356 Acid_5944 Acid345_4622 | |
| LUAcid_KM4_H7_29 | 25551 | 26975 | | | amidophosphoribosyl transferase (PurF) | | 1 | D | ADDED | | 2.4.2.14 | | - best match to 41b15_012 PurF AY281356 (71% id) - purin biosynthesis operon - also COG0449 - Purine nucleotides are synthesised both via the de novo pathway and via the salvage pathway and are vital for cell functions and cell proliferation through DNA and RNA syntheses and ATP energy supply. Amidophosphoribosyltransferase (EC:2.4.2.14) is the rate-limiting enzyme in the de novo pathway of purine ribonucleotide synthesis and is regulated by feedback inhibition by AMP and GMP [1]. | PROTEIN | COG0034 Glutamine phosphoribosylpyrophosphate amidotransferase | F Nucleotide transport and metabolism | Good | ABE | 82.227.62.180 | 18/09/07 16:25:16 | several othologs in Acidobacteria LUAcid_KM3_G1_07 LUAcid_KM3_D9_18 L35511_KM3_47_B8_405 L35498_AD55_D2_302 LUAcid_AD106_G4_13 LUAcid_KM4_H7_29 41b15_012 PurF AY281356 23k22_008 PurF AY281352 Acid345_4621 Acid_5945 | |
| LUAcid_KM4_H7_19 | 14136 | 15416 | | | phosphoribosylamineglycine ligase (PurD) | | 1 | D | ADDED | | | | - best match to 23k22_017 (58% id) | PROTEIN | COG0151 Phosphoribosylamine-glycine ligase | F Nucleotide transport and metabolism | Good | ABE | 82.227.62.180 | 18/09/07 17:02:29 | present on soil clones and one copy in both genomes: LUAcid_KM4_H7_19 23k22_017 PurD AY281352 41b15_020 PurD AY281356 Acid345_0231 Acid_0014 | |
| LUAcid_KM4_H7_20 | 15472 | 15972 | | | phosphoribosylaminoimidazole carboxylase (PurE) | | 1 | D | ADDED | | | | - best match to 23k22_016 PurE (62% id) - Purin biosynthesis operon - synonyme Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase - present also in E but affiliation AB | PROTEIN | COG0041 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase | F Nucleotide transport and metabolism | Good | AB | 82.227.62.180 | 18/09/07 17:09:29 | - one match in both genomes - match to 23k22_016 PurE ;AY281352 - absent in 41b15 | |
| LUAcid_KM4_H7_18 | 13957 | 13757 | | | 30S Ribosomal protein S21 | | 1 | R | ADDED | | | | - best match to 30S ribosomal protein 23k22_018 AY281352 (?id) - IPR001911 Ribosomal protein S21 | PROTEIN | | | - | B | 82.227.62.180 | 18/09/07 17:15:46 | - ortholog in 23k22_018 AY281352 | |
| LUAcid_KM4_H7_17 | 13528 | 12641 | | | prenyltransferase-like protein | | 1 | R | ADDED | | | | - best match to 23k22_022 AY281352 (56% id) - no COG - Molecular Function:prenyltransferase activity - IPR000537 UbiA prenyltransferase - membrane protein - UbiA prenyltransferase domain | PROTEIN | | | Good | ABE | 82.227.62.180 | 18/09/07 17:27:16 | ortholog to soil clone proteins: 23k22_022 AY281352 (56% id) 41b15_023 AY281356 | |
| LUAcid_KM4_H7_16 | 12625 | 11498 | | | protein of unknown function DUF362 | | 1 | R | ADDED | | | | - best match to hypothetical protein Mbar_A1412 Methanosarcina barkeri str. Fusaro (50% id) - no COG | PROTEIN | | | Good | AB | 82.227.62.180 | 18/09/07 18:10:59 | no match in both acidobacterial genomes - strong match to 23k22_023 AY281352 (43% id), not to 41b15 | |
| LUAcid_KM4_H7_15 | 11431 | 10586 | | | hypothetical protein | | 1 | R | ADDED | | | | - best match to 41b15_024 AY281356 (38% id) - no COG - no domain | PROTEIN | | | Good | unique | 82.227.62.180 | 18/09/07 18:14:09 | - match to 41b15_024 AY281356 (38% id) | |
| LUAcid_KM4_H7_12 | 10078 | 9428 | | | 2OG-Fe(II) oxygenase like protein | | 1 | R | ADDED | | | | - InterPro relationship to Alkylated DNA repair protein AlkB - not in Archaea | PROTEIN | COG3145 Alkylated DNA repair protein | L Replication, recombination and repair | - | AE | 82.227.62.180 | 18/09/07 18:27:48 | match to one ORF in the both acidobacterial genomes; no match in clones | |
| LUAcid_KM4_H7_11 | 9390 | 8884 | | | conserved hypothetical protein | | 1 | R | ADDED | | | | - best match to Burkholderia phymatum STM815 (42%) - no COG - low phospholipid domain (pfam04972) - in B and E | PROTEIN | | | Good but overlapping | | 82.227.62.180 | 18/09/07 18:33:23 | - no match to Acidobacteria | |
| LUAcid_KM4_H7_10 | 8574 | 8891 | | | antibiotic biosynthesis monooxygenase family enzyme | | 1 | D | ADDED | | | | - best match to Rhodoferax ferrireducens T118 (76% id) - only 7 matches: Rhodoferax, Alcanivorax, Marinobacter algicola DG893, Idiomarina, Marinobacter sp. ELB17, Marinobacter aquaeolei, marine gamma proteobacterium HTCC2080 - conserved ony in a small group of Bacteria: beta, gamma protobacteria and here Acidobacteria | PROTEIN | | | - | | 82.227.62.180 | 18/09/07 18:43:56 | - no match to Acidobacteria | |
| LUAcid_KM4_H7_10 | 8574 | 8891 | | | antibiotic biosynthesis monooxygenase family enzyme | | 1 | D | ADDED | | | | - best match to Rhodoferax ferrireducens T118 (76% id) - only 7 matches: Rhodoferax, Alcanivorax, Marinobacter algicola DG893, Idiomarina, Marinobacter sp. ELB17, Marinobacter aquaeolei, marine gamma proteobacterium HTCC2080 - conserved ony in a small group of Bacteria: beta, gamma protobacteria and here Acidobacteria - This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species, which can carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. | PROTEIN | | | - | | 82.227.62.180 | 18/09/07 18:47:51 | - no match to Acidobacteria | |
| LUAcid_KM4_H7_09 | 7894 | 8514 | | | conserved hypothetical protein | | 1 | D | ADDED | | | | - best match to Rhodoferax ferrireducens T118 (65% id) - present in a relatively small number of Bacteria, i.e. Rhodoferax, Burkholderia, Polaromonas naphthalenivorans... - no COG - interPro- no domain | PROTEIN | | | - | | 82.227.62.180 | 18/09/07 18:58:47 | - no match to Acidobacteria - environment to be verified | |
| LUAcid_KM4_H7_08 | 7781 | 7185 | | | NADPH-dependent FMN reductase | | 1 | R | ADDED | | 1.5.1.29 | | - very strong match to Polaromonas naphthalenivorans CJ2 (87% id) - very conserved protein - orthologs also in AEB, but affiliation to B | PROTEIN | COG0431 Predicted flavoprotein | R General function prediction only | Good but overlapping | AB | 82.227.62.180 | 19/09/07 09:25:05 | - low matches in both acidobacterial genomes - not in clones - environment conserved at least in Paloromonas --> to be analysed | |
| LUAcid_KM4_H7_07 | 6460 | 7104 | | | acyl carrier protein phosphodiesterase | | 1 | D | ADDED | | | | - very high similarity to Polaromonas naphthalenivorans CJ2 (85% id) - flavodoxin-like fold domaine - occurence also iin A and E | PROTEIN | COG1182 Acyl carrier protein phosphodiesterase | I Lipid transport and metabolism | - | B | 82.227.62.180 | 19/09/07 09:34:22 | - no matches in Acidobacteria - environment conserved with previous protein in Paloromonas | |
| LUAcid_KM4_H7_06 | 6232 | 5330 | | | transcriptional regulator, LysR family | | 1 | R | ADDED | | | | - high similarity to Polaromonas naphthalenivorans CJ2 (76% id) - Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif -IPR000847 Bacterial regulatory protein, LysR | PROTEIN | COG0583 Transcriptional regulator | K Transcription | - | B | 82.227.62.180 | 19/09/07 09:40:25 | - low matches in both genomes - not in other clones - environment conserved in Polaromonas | |
| LUAcid_KM4_H7_05 | 5104 | 4091 | | | Thiosulphate-binding protein | | 1 | R | ADDED | | | | - very similar to Polaromonas sp. JS666 (85% id) | PROTEIN | COG1613 ABC-type sulfate transport system, periplasmic component | P Inorganic ion transport and metabolism | - | B | 82.227.62.180 | 19/09/07 09:54:17 | - no match in Acidobacteria - enironment conserved in Burkholderia; to be verified - part of operon like organisation in Bacteria | |
| LUAcid_KM4_H7_04 | 4084 | 3209 | | | sulfate ABC transporter, inner membrane subunit CysT | | 1 | R | ADDED | | | | - high similarity to Polaromonas sp. JS666 (85% id) - highly conserved protein in B - Binding-protein-dependent transport systems inner membrane component - large group of transporter in A, B, and E - sulfate transmembrane transporter activity - integral membrane protein - COG affiliation sounds strange? | PROTEIN | COG0555 ABC-type sulfate transport system, permease component | O Posttranslational modification, protein turnover, chaperones | Good but overlapping | B | 82.227.62.180 | 19/09/07 10:01:23 | - paralog to adjacent protein on KM4_9_H7_323 and 330 - lower matches in acidobacterial genomes | |
| LUAcid_KM4_H7_03 | 3209 | 2301 | | | sulfate ABC transporter, inner membrane subunit CysW | | 1 | R | ADDED | | | | - high similarity to Polaromonas sp. JS666 (74% id) - second subunit of sulfate transporter | PROTEIN | COG4208 ABC-type sulfate transport system, permease component | P Inorganic ion transport and metabolism | - | B | 82.227.62.180 | 19/09/07 10:05:44 | - similarity to adjacent protein; two different subunits - environment conserved? | |
| LUAcid_KM4_H7_04 | 4084 | 3209 | | | sulfate ABC transporter, inner membrane subunit CysT | | 1 | R | ADDED | | | | - high similarity to Polaromonas sp. JS666 (85% id) - highly conserved protein in B - Binding-protein-dependent transport systems inner membrane component - large group of transporter in A, B, and E - sulfate transmembrane transporter activity - integral membrane protein - COG affiliation sounds strange? | PROTEIN | COG0555 ABC-type sulfate transport system, permease component | O Posttranslational modification, protein turnover, chaperones | Good but overlapping | B | 82.227.62.180 | 19/09/07 10:07:17 | - similarity to adjacent protein on KM4_9_H7_323 (CysT su) and 330 (CysW su) - lower matches in acidobacterial genomes | |
| LUAcid_KM4_H7_02 | 2274 | 1192 | | | sulfate ABC transporter, ATPase subunit | | 37 | R | ADDED | | | | - very similar to Polaromonas naphthalenivorans CJ2 (80% id) - highly conserved in B | PROTEIN | COG1118 ABC-type sulfate/molybdate transport systems, ATPase component | P Inorganic ion transport and metabolism | Good but overlapping | B | 82.227.62.180 | 19/09/07 10:11:12 | - several matches in both acidobacterial genomes - operon-like organisation? | |
| LUAcid_KM4_H7_01 | 950 | 432 | | | Disulphide bond formation protein DsbB | | 28 | R | ADDED | | | | - high similarity to Polaromonas sp. JS666 (72% id) - disulphide oxidoreductase - conserved in B - group of protein affiliated to proteobacteria | PROTEIN | COG1495 Disulfide bond formation protein DsbB | O Posttranslational modification, protein turnover, chaperones | Good | B | 82.227.62.180 | 19/09/07 10:18:40 | - no matches in Acidobacteria - environment conserved in Brukholderia? | |
| LUAcid_KM4_H7_14 | 10586 | 10272 | | | truncated hexosyltransferase | | 1 | R | ADDED | | | | - only N-terminal matches to hexosyltransgferases (approx. 80aa) | PROTEIN | | | - | | 82.227.62.180 | 19/09/07 11:34:27 | - N-terminal match to 41b15_025 AY281356 putative hexosyltransferase | |
| LUAcid_KM4_H7_13 | 10375 | 10133 | | | hypothetical protein | | 1 | R | ADDED | | | | - C-terminal best match to Polaromonas (91% id C-terminal, 70aa); truncated of 160aa | PROTEIN | | | - | | 82.227.62.180 | 19/09/07 11:42:35 | C-terminal good matches to conserved hypothetical proteins in both acidobacterial genomes (Acid_4008) (78% id in the matched region of 70aa) - C-terminal COG3826 - to be revised | |
| LUAcid_KM4_H7_30 | 27099 | 28127 | | | phosphoribosylformylglycinamidine cyclo ligase (PurM) | | 1 | D | ADDED | | | | - IPR000728 AIR synthase related protein - purin biosynthesis operon | PROTEIN | COG0150 Phosphoribosylaminoimidazole (AIR) synthetase | F Nucleotide transport and metabolism | Good | | 82.227.62.180 | 21/09/07 10:28:18 | - environment conserved in Acidobacteria - to be verified | |
| LUAcid_KM4_H7_31 | 28127 | 28765 | | | phosphoribosylglycinamide formyltransferase (PurN) | | 1 | D | ADDED | | | | - purin biosynthesis operon | PROTEIN | COG0299 Folate-dependent phosphoribosylglycinamide formyltransferase PurN | F Nucleotide transport and metabolism | Good | | 82.227.62.180 | 21/09/07 10:29:44 | - environment conserved in Acidobacteria | |
| LUAcid_KM4_H7_32 | 29629 | 28781 | | | conserved hypothetical protein | | 1 | R | ADDED | | | | PR004843 Metallophosphoesterase domain | PROTEIN | COG1408 Predicted phosphohydrolases | R General function prediction only | Good | | 82.227.62.180 | 21/09/07 10:32:34 | - environment conserved in Acidobacteria - to be verified - match to soil clone 23k22_002 | |
| LUAcid_KM4_H7_33 | 29694 | 30941 | | | tyrosyl-tRNA synthetase | | 1 | D | ADDED | | 6.1.1.1 | | | PROTEIN | COG0162 Tyrosyl-tRNA synthetase | J Translation, ribosomal structure and biogenesis | Good | ABE | 82.227.62.180 | 21/09/07 10:34:06 | - environment conserved in Acidobacteria - to be verified | |
| LUAcid_KM4_H7_23 | 18581 | 19897 | | | peptidase M16 domain protein | | 1 | D | ADDED | | | | - adjacent to purin biosynthesis operon - IPR001431 Peptidase M16, zinc-binding site - not in A | PROTEIN | COG0612 Predicted Zn-dependent peptidases | R General function prediction only | Good | B | 82.227.62.180 | 1/10/07 11:33:01 | - several matches in acidobacterial clones (soil and marine) - environment conserved? - to be verified | |
| LUAcid_KM4_H7_22 | 18394 | 17357 | | | radical SAM enzyme, Cfr family | | 1 | R | ADDED | | | | - adjacent to purin biosynthesis operon - IPR004383 Conserved hypothetical protein 48 - not in A - not in A | PROTEIN | COG0820 Predicted Fe-S-cluster redox enzyme | R General function prediction only | Good | B | 82.227.62.180 | 1/10/07 11:38:55 | - several matches in acidobacterial clones (soil and marine) - environment conserved? - to be verified | |
| LUAcid_KM4_H7_21 | 15972 | 17252 | | | MiaB-like tRNA modifying enzyme | | 1 | D | ADDED | | | | - adjacent to purin biosynthesis operon - IPR005839 Protein of unknown function UPF0004 - Elongator protein 3/MiaB/NifB - Radical SAM domain - not in A | PROTEIN | COG0621 2-methylthioadenine synthetase | J Translation, ribosomal structure and biogenesis | Good | ABE | 82.227.62.180 | 1/10/07 11:41:28 | - several matches in acidobacterial clones (soil and marine) - environment conserved? - to be verified | |
| LUACID_KM4_H7_32 | 29629 | 28781 | | | Metallophosphoesterase | | 1 | R | ADDED | | | | PR004843 Metallophosphoesterase domain | PROTEIN | COG1408 Predicted phosphohydrolases | R General function prediction only | Good | | 82.227.62.180 | 9/10/07 09:50:05 | - environment conserved in Acidobacteria - to be verified - match to soil clone 23k22_002 | |
| LUACID_KM4_H7_07 | 6460 | 7104 | | | acyl carrier protein phosphodiesterase | | 1 | D | ADDED | | | | - very high similarity to Polaromonas naphthalenivorans CJ2 (85% id) - flavodoxin-like fold domaine - occurence also iin A and E - could be an Azoreductase involved in Mordant yellow 3 pathway (industrial dye biodegradation | PROTEIN | COG1182 Acyl carrier protein phosphodiesterase | I Lipid transport and metabolism | - | B (only bacteria) | 82.227.62.180 | 9/10/07 11:22:06 | - no matches in Acidobacteria - environment conserved with previous protein in Paloromonas | |
| LUACID_KM4_H7_16SRNA | 31242 | 32803 | | | 16S ribosomal RNA | | 1 | D | ADDED | 16SrRNA | | | | RNA | | | - | | 129.175.105.75 | 29/10/07 18:30:27 | | |
| LUACID_KM4_H7_23SRNA | 33403 | 34997 | | | 23S ribosomal RNA | | 1 | D | ADDED | 23SrRNA | | | | RNA | | | | | 129.175.105.75 | 29/10/07 18:31:02 | | |
| LUACID_KM4_H7_TRNA1 | 33058 | 33131 | | | tRNA-Ile (GAT) | | 1 | D | ADDED | tRNA-Ile | | | | TRNA | | | | | 129.175.105.75 | 29/10/07 18:32:00 | | |
| LUACID_KM4_H7_TRNA2 | 33148 | 33220 | | | tRNA-Ala (TGC) | | 1 | R | ADDED | tRNA-Ala | | | | TRNA | | | | | 129.175.105.75 | 29/10/07 18:32:33 | | |
| LUACID_KM4_H7_17 | 13528 | 12641 | | | prenyltransferase-like protein | | 1 | R | ADDED | | | | - best match to 23k22_022 AY281352 (56% id) - no COG - Molecular Function:prenyltransferase activity - IPR000537 UbiA prenyltransferase - membrane protein - UbiA prenyltransferase domain | PROTEIN | COG0382 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases | H Coenzyme transport and metabolism | Good | ABE | 129.175.105.75 | 17/12/07 16:41:35 | ortholog to soil clone proteins: 23k22_022 AY281352 (56% id) 41b15_023 AY281356 fixed COG -yz | |
| LUACID_KM4_H7_13 | 10375 | 10133 | | | hypothetical protein | | 1 | R | ADDED | | | | - C-terminal best match to Polaromonas (91% id C-terminal, 70aa); truncated of 160aa | PROTEIN | COG3826 Uncharacterized protein conserved in bacteria | S Function unknown | - | | 129.175.105.75 | 17/12/07 17:26:00 | fixed COG -yz | |
| LUACID_KM4_H7_14 | 10586 | 10272 | | | truncated hexosyltransferase | | 1 | R | ADDED | | | | - only N-terminal matches to hexosyltransgferases (approx. 80aa) | PROTEIN | COG0038 Chloride channel protein EriC | P Inorganic ion transport and metabolism | - | | 129.175.105.75 | 17/12/07 17:31:23 | - N-terminal match to 41b15_025 AY281356 putative hexosyltransferase fixed COG -yz |