| 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 | |
| | | | | | | | | | | | | | | | | | | | | 10/10/03 00:00:00 | | |
| LUAcid_AD370_D1_01 | 1595 | 372 | | | ABC efflux pump, inner membrane subunit | | 1 | R | ADDED | | | | - best match to Acidobacteria bacterium Ellin345 (35% identity) - matches in Bacteria, not A and not E - also CO0318 IQ lipid transport and metabolism - no matches on other clones - length good start GTG | PROTEIN | COG0577 ABC-type antimicrobial peptide transport system, permease component | V Defense mechanisms | Good | | 82.227.62.180 | 14/09/07 14:00:14 | | |
| LUAcid_AD370_D1_02 | 2248 | 1751 | | | hypothetical protein | | 1 | R | ADDED | | | | - best and single in database match to Acid_6477 solibacter (50% identity) --> unique in subgroup of Acidobacteria - no matches to other acidobacterial clones - | PROTEIN | | | Good | unique | 82.227.62.180 | 14/09/07 14:04:14 | | |
| LUAcid_AD370_D1_03 | 2446 | 4167 | | | gamma-glutamyltransferase | | 2 | D | ADDED | | | | - best match Solibacter Acid_2807 (54% identity) - present on other clones:KM3_187_G1_308; AD106_G4_404, KM3_47_B8_164; AD55_D2_062 - in all kind of Bacteria | PROTEIN | COG0405 Gamma-glutamyltransferase | E Amino acid transport and metabolism | Good | B | 82.227.62.180 | 14/09/07 14:23:45 | | |
| LUAcid_AD370_D1_04 | 5288 | 4245 | | | hypothetical protein | | 1 | R | ADDED | | | | - low similarity to putative type IV pilin secretion protein [Haemophilus influenzae PittGG] only 27% identity and different length | PROTEIN | | | Good | unique | 82.227.62.180 | 14/09/07 14:26:23 | | |
| LUAcid_AD370_D1_05 | 11353 | 13011 | | | cotransporter/symporter protein | | 50 | D | ADDED | | | | - best match to Bacteroides thetaiotaomicron VPI-5482 (52% identity) - conserved in CFB group of Bacteria and Eukaryotes - low matches in both Ellin345 and Ellin6706 - low match to KM3_18_F8_238 - start changed to 50aa, ORF too long | PROTEIN | COG4146 Predicted symporter | R General function prediction only | Good | BE | 82.227.62.180 | 14/09/07 15:35:22 | | |
| LUAcid_AD370_D1_06 | 13125 | 13664 | | | protein of unknown function DUF177 | | 1 | D | ADDED | | | | - best match to Solibacter usitatus Ellin6076 (38% id) - one match in each acido genome - not in other clones - length OK | PROTEIN | COG1399 Predicted metal-binding, possibly nucleic acid-binding protein | R General function prediction only | Good | B | 82.227.62.180 | 14/09/07 17:49:05 | - envirnoment conserved in Ellin345 and Ellin6706 and cloneAD370_D1_152? - and in addition ribosomal protein L32 - DUF177, Rib L12, fatty acid synthase in syntheny in Acidobacteria and also in other Bacteria: Geobacter, Pelobacter.... | |
| LUAcid_AD370_D1_07 | 13703 | 13882 | | | ribosomal protein L32 | | 1 | D | ADDED | | | | - best match Acid345_4144 (60% id) - very conserved in B - Pfam1783 | PROTEIN | | | - | B | 82.227.62.180 | 14/09/07 17:57:22 | - envirnoment conserved in Ellin345 and Ellin6706 and cloneAD370_D1_152? - and in addition ribosomal protein L32 - DUF177, Rib L12, fatty acid synthase in syntheny in Acidobacteria and also in other Bacteria: Geobacter, Pelobacter.... | |
| LUAcid_AD370_D1_08 | 13953 | 14975 | | | fatty acid/phospholipid synthesis protein PlsX | | 1 | D | ADDED | | | | - present in both acido genomes - best match Solibacter (64% identity) - Acid_6758 and Acid345_4145 - also COG0365 | PROTEIN | COG0416 Fatty acid/phospholipid biosynthesis enzyme | I Lipid transport and metabolism | Good | B | 82.227.62.180 | 14/09/07 18:02:10 | - environment conserved in Ellin345 and Ellin6706 and cloneAD370_D1_152? - and in addition ribosomal protein L32 - DUF177, Rib L12, fatty acid synthase in syntheny in Acidobacteria and also in other Bacteria: Geobacter, Pelobacter.... | |
| LUAcid_AD370_D1_09 | 15770 | 14985 | | | acyl-(acyl-carrier-protein)--UDP-N-acetylglucosamine O-acyltransferase | | 1 | R | ADDED | | | | - best match Solibacter usitatus Ellin6076 (42% Id) - also COG1044 - IPR001451: bacterial transferase domain ”hexapep” | PROTEIN | COG1043 Acyl-[acyl carrier protein]--UDP-N-acetylglucosamine O-acyltransferase | M Cell wall/membrane/envelope biogenesis | Good | B | 82.227.62.180 | 14/09/07 18:09:31 | - environment not conserved - not in other acido clones | |
| LUAcid_AD370_D1_10 | 16780 | 15863 | | | conserved hypothetical protein | | 1 | R | ADDED | | | | - best match to Bacillus (34%) - DNA repair photolyase annotation and COG? - DUF85 and Radical_SAM domain - also COG0440 amino acid transport and metabolism? - one low match in Methanogen (Archaea) - length OK | PROTEIN | COG1533 DNA repair photolyase | L Replication, recombination and repair | Good | B | 82.227.62.180 | 14/09/07 18:26:02 | - one copy in each acidobacterial genome | |
| LUAcid_AD370_D1_12 | 17820 | 17518 | | | conserved hypothetical | | 1 | R | ADDED | | | | - Antibiotic biosynthesis monooxygenase ? - best match Geobacter bemidjiensis Bem (51% id) - length OK - good - low matches in A and E | PROTEIN | COG1359 Uncharacterized conserved protein | S Function unknown | Good | B | 82.227.62.180 | 14/09/07 18:36:23 | - no match in clones and Acido genomes | |
| LUAcid_AD370_D1_11 | 17437 | 16919 | | | hypothetical protein | | 66 | R | ADDED | | | | - thioredoxin domain - best match to Geobacter (28% id) - start changed to 66aa to eliminate overhang | PROTEIN | | | Good but overlapping | B | 82.227.62.180 | 14/09/07 18:43:24 | - very low match to Acidobacteria in genomes | |
| LUAcid_AD370_D1_13 | 19041 | 17842 | | | hypothetical protein (neuramidase related) | | 1 | R | ADDED | | | | - best match Flavobacterium sp. MED217 (37% id) - length OK - low match in Oryza (Rice) - sialidase/neuramidase domaine | PROTEIN | | | Good | B | 82.227.62.180 | 14/09/07 18:50:55 | - not in acidobacteria | |
| LUAcid_AD370_D1_14 | 19147 | 19701 | | | translation elongation factor P | | 17 | D | ADDED | | | | - best match Solibacter (63% id) - second Ellin345 - start codon to 17aa adaptation to lenght of others | PROTEIN | COG0231 Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) | J Translation, ribosomal structure and biogenesis | Good but overlapping | B | 82.227.62.180 | 14/09/07 19:02:29 | - two matches in each acidobacterial genome - not on clones - but on environmental clone translation elongation factor P [uncultured bacterium 105] locus AAR37444 (Delong) | |
| LUAcid_AD370_D1_15 | 20388 | 19747 | | | hypothetical protein | | 1 | R | ADDED | | | | - low similarity to Tat (twin-arginine translocation) pathway signal sequence domain protein - TAT_signal domain - length OK | PROTEIN | | | Good | B | 82.227.62.180 | 14/09/07 19:54:05 | - low similarity to Acid7383 and KM3_B4__029 | |
| LUAcid_AD370_D1_16 | 22093 | 20384 | | | glucose-methanol-choline oxidoreductase | | 1 | R | ADDED | | | | - best match Solibacter usitatus Ellin6076 (50% Id) - also COG0765 - NAD and FAD binding domain - Oxidoreductase family - 2 matches also in Halobacteriaceae | PROTEIN | COG2303 Choline dehydrogenase and related flavoproteins | E Amino acid transport and metabolism | Good | B | 82.227.62.180 | 14/09/07 20:01:02 | - several matches in geacido genome sequences - match in KM3_25_B4 | |
| LUAcid_AD370_D1_17 | 23664 | 22174 | | | glycerol kinase | | 1 | R | ADDED | | | | - best match to Deinococcus geothermalis (55% id) - highly conserved in B - also COG0017 and COG1070 - carbohydrate kinase related | PROTEIN | COG0554 Glycerol kinase | C Energy production and conversion | Good | B | 82.227.62.180 | 14/09/07 20:05:32 | - two good matches in each genome - not in clones | |
| LUAcid_AD370_D1_18 | 23760 | 24392 | | | conserved hypothetical protein | | 1 | D | ADDED | | | | - best match to Acid3195 (40% id) - predicted hydrolase of alpha/beta superfamily | PROTEIN | COG2945 Predicted hydrolase of the alpha/beta superfamily | R General function prediction only | Good | B | 82.227.62.180 | 14/09/07 20:11:48 | - one match in each genome - not on clones - environment not conserved | |
| LUAcid_AD370_D1_19 | 25416 | 24427 | | | acetamidase/formamidase | | 1 | R | ADDED | | | | - best match to Aurantimonas sp. SI85-9A1 (49% id) - conserved protein | PROTEIN | COG2421 Predicted acetamidase/formamidase | C Energy production and conversion | Good | ABE | 82.227.62.180 | 14/09/07 20:18:26 | - good matches in Ellin6706 but not in Acid345 | |
| LUAcid_AD370_D1_20 | 25976 | 25533 | | | putative ribosomal-protein acetyltransferase | | 1 | R | ADDED | | | | - Burkholderia pseudomallei (32% id) - one match in Methonpyrus (Euryarchaeota) | PROTEIN | COG0456 Acetyltransferases | R General function prediction only | Good | B | 82.227.62.180 | 14/09/07 20:49:40 | - one match in the two genomes - low similarity to KM3_47_B8_104 | |
| LUAcid_AD370_D1_21 | 26198 | 27133 | | | Sulfite oxidase-like enzyme | | 34 | D | ADDED | | | | - best match to uncultured organism (53% id) from ”Construction and analysis of a metagenomic library from a deep-sea sediment of east Pacific nodule Province - next match Methylobacterium - oxidoreductase, molybdopterin binding domain - start codon to 34aa, adaptation to length of others | PROTEIN | COG2041 Sulfite oxidase and related enzymes | R General function prediction only | Good | B | 82.227.62.180 | 14/09/07 21:00:08 | - one good match in the both sequenced genomes and 2 lower matches (45% id) - no match on clones - interesting match from uncultured deep sea | |
| LUAcid_AD370_D1_22 | 27392 | 28273 | | | dTDP-4-dehydrorhamnose reductase | | 22 | D | ADDED | | 1.1.1.133 | | - best match Solibacter usitatus (49% id) - start to 22aa - extracellular polysaccharide biosynthetic process | PROTEIN | COG1091 dTDP-4-dehydrorhamnose reductase | M Cell wall/membrane/envelope biogenesis | Good | AB | 82.227.62.180 | 14/09/07 21:08:50 | - similar to Acid_6228 - environment not conserved | |
| LUAcid_AD370_D1_23 | 28737 | 28276 | | | single-strand binding protein | | 13 | R | ADDED | | | | - best match to Solibacter usitatus Ellin6076 (51% id) | PROTEIN | COG0629 Single-stranded DNA-binding protein | L Replication, recombination and repair | Good | B | 82.227.62.180 | 14/09/07 21:54:08 | - one match in the two genomes - not on clones | |
| LUAcid_AD370_D1_24 | 29643 | 28858 | | | molybdenum ABC transporter molybdenum-binding protein | | 1 | R | ADDED | | | | - best match to Symbiobacterium thermophilum (40% id) - conserved | PROTEIN | COG0725 ABC-type molybdate transport system, periplasmic component | P Inorganic ion transport and metabolism | Good | AB | 82.227.62.180 | 14/09/07 21:59:06 | - one match in the two genomes - not in clones | |
| LUAcid_AD370_D1_25 | 29822 | 31030 | | | major facilitator superfamily MFS_1 | | 1 | D | ADDED | | | | - best match to Parvibaculum lavamentivorans (23% id) | PROTEIN | COG0477 Permeases of the major facilitator superfamily | G Carbohydrate transport and metabolism | Good | ABE | 82.227.62.180 | 14/09/07 22:05:45 | - very low match in both genomes | |
| LUAcid_AD370_D1_26 | 32626 | 31142 | | | protein of unknown function DUF1501 | | 1 | R | ADDED | | | | - best match to Planctomyces maris DSM 8797 (52% id) - very high number of paralogs in each genome with orthologs (Planctomycetes 64 hits) - only present in a small number of Bacteria...Poribacteria... | PROTEIN | | | Good | B | 82.227.62.180 | 14/09/07 22:20:17 | - strong similarities to KM3_18_F8_163 and KM3_18_F8_128 - several paralogs (10+) in Solibacter, not in Elllin345 - often in tandem with DUF1549 protein as on clone KM3_18_F8 ORF128 and 116 - here not in tandem - ortholog on Poribacteria fragment | |
| LUAcid_AD370_D1_27 | 32796 | 34130 | | | glutamate-1-semialdehyde-2,1-aminomutase | | 1 | D | ADDED | | 5.4.3.8 | | - best match to Lentisphaera araneosa (47%) - very conserved protein in bacteria and archaea - also COG4992 and COG0160 | PROTEIN | COG0001 Glutamate-1-semialdehyde aminotransferase | H Coenzyme transport and metabolism | Good | AB | 82.227.62.180 | 14/09/07 22:29:17 | - good match on the two genomes - ortholog to KM3_18_F8_249 | |
| LUAcid_AD370_D1_28 | 34222 | 35229 | | | N-acetyl-gamma-glutamyl-phosphate reductase | | 1 | D | ADDED | | 1.2.1.38 | | - best match to Solibacter usitatus (62% id) - very conserved in bacteria but also in Archaea | PROTEIN | COG0002 Acetylglutamate semialdehyde dehydrogenase | E Amino acid transport and metabolism | Good | AB | 82.227.62.180 | 14/09/07 22:36:41 | - one ortholog on the two genomes - not on clones | |
| LUAcid_AD370_D1_29 | 35263 | 36039 | | | acetylglutamate kinase | | 1 | D | ADDED | | 2.7.2.8 | | - best match to Solibacter usitatus (51% id) - often in tandem with glutamate-1-semialdehyde-2,1-aminomutase as here with 346 | PROTEIN | COG0548 Acetylglutamate kinase | E Amino acid transport and metabolism | Good | AB | 82.227.62.180 | 14/09/07 22:45:23 | - one match on the two genomes | |
| LUAcid_AD370_D1_30 | 36292 | 36603 | | | putative regulatory protein, FmdB family | | 1 | D | ADDED | | | | - best match to Solibacter usitatus (55% id) | PROTEIN | COG2331 Uncharacterized protein conserved in bacteria | S Function unknown | Good | B | 82.227.62.180 | 14/09/07 22:54:56 | - one good match in the two genomes - lower match in KM3_205_D9_425 | |
| LUAcid_AD370_D1_31 | 37575 | 38174 | | | threonyl-tRNA synthetase (truncated c-terminal) | | 1 | D | ADDED | | | | - best match to Acidobacteria bacterium (54% id) | PROTEIN | COG0441 Threonyl-tRNA synthetase | J Translation, ribosomal structure and biogenesis | Good | | 82.227.62.180 | 14/09/07 22:58:57 | - one match in the two genomes | |
| LUACID_AD370_D1_01 | 1595 | 372 | | | ABC efflux pump, inner membrane subunit, DUF214 | | 1 | R | ADDED | | | | - best match to Acidobacteria bacterium Ellin345 (35% identity) - matches in Bacteria, not A and not E - also CO0318 IQ lipid transport and metabolism - no matches on other clones - length good start GTG | PROTEIN | COG0577 ABC-type antimicrobial peptide transport system, permease component | V Defense mechanisms | Good | B (only bacteria) | 82.227.62.180 | 12/10/07 17:19:28 | | |
| LUACID_AD370_D1_16SRNA | 5884 | 7399 | | | 16S ribosomal RNA | | 1 | D | ADDED | 16SrRNA | | | | RNA | | | | | 129.175.105.75 | 29/10/07 17:29:56 | | |
| LUACID_AD370_D1_23SRNA | 8054 | 10884 | | | 23S ribosomal RNA | | 1 | D | ADDED | 23SrRNA | | | | RNA | | | | | 129.175.105.75 | 29/10/07 17:30:20 | | |
| LUACID_AD370_D1_5SRNA | 11148 | 11240 | | | 5S ribosomal RNA | | 1 | D | ADDED | 5SrRNA | | | | RNA | | | | | 129.175.105.75 | 29/10/07 17:31:01 | | |
| LUACID_AD370_D1_TRNA1 | 7588 | 7660 | | | tRNA-Ala (TGC) | | 1 | D | ADDED | tRNA-Ala | | | | TRNA | | | | | 129.175.105.75 | 29/10/07 17:32:31 | | |
| LUACID_AD370_D1_TRNA2 | 7691 | 7764 | | | tRNA-Ile (GAT) | | 1 | D | ADDED | tRNA-Ile | | | | TRNA | | | | | 129.175.105.75 | 29/10/07 17:33:01 | | |
| LUACID_AD370_D1_21 | 26198 | 27133 | | | oxidoreductase, molybdopterin binding domain | | 34 | D | ADDED | | | | - best match to uncultured organism (53% id) from iConstruction and analysis of a metagenomic library from a deep-sea sediment of east Pacific nodule Province - next match Methylobacterium - oxidoreductase, molybdopterin binding domain - start codon to 34aa, adaptation to length of others | PROTEIN | COG2041 Sulfite oxidase and related enzymes | R General function prediction only | Good | B (only bacteria) | 82.227.62.180 | 29/11/07 09:29:09 | - one good match in the both sequenced genomes and 2 lower matches (45% id) - no match on clones - interesting match from uncultured deep sea | |
| LUACID_AD370_D1_14 | 19147 | 19701 | | | translation elongation factor P | | 17 | D | ADDED | ef-P | | | - best match Solibacter (63% id) - second Ellin345 - start codon to 17aa adaptation to lenght of others | PROTEIN | COG0231 Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) | J Translation, ribosomal structure and biogenesis | Good but overlapping | B (only bacteria) | 129.175.105.75 | 30/01/08 17:48:19 | - two matches in each acidobacterial genome - not on clones - but on environmental clone translation elongation factor P [uncultured bacterium 105] locus AAR37444 (Delong) |