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_KM3_B4_22 | 32155 | 33651 | | | Glucose-methanol-choline oxidoreductase family protein | | 11 | D | ADDED | | | | - best match to Nitrobacter hamburgensis X14 (33% id) - start change to 11aa - truncated C-terminal of approximately 70aa - gluconate DH | PROTEIN | COG2303 Choline dehydrogenase and related flavoproteins | E Amino acid transport and metabolism | Good | B | 82.227.62.180 | 15/09/07 09:00:39 | - 7 matches to Solibacter - one match to Acid345 - one match to AD370_D1_227 | |
LUAcid_KM3_B4_21 | 31434 | 32162 | | | hypothetical protein | | 47 | D | ADDED | | | | - best match Ralstonia metallidurans CH34 (29% id) - start to 47aa after length comparison and overlap consideration | PROTEIN | | | Good but overlapping | BE | 82.227.62.180 | 15/09/07 09:12:41 | - low matches in acidobacterial genomes - very low match to AD370_D1_209 - environment conserved with gluconate DH in several bacteria (Ralstonia...) | |
LUAcid_KM3_B4_20 | 30860 | 31387 | | | phosphatidylethanolamine-binding protein | | 21 | D | ADDED | | | | - best match to Syntrophus aciditrophicus (39% id) - start to 21aa, after length comparison | PROTEIN | COG1881 Phospholipid-binding protein | R General function prediction only | Good | ABE | 82.227.62.180 | 15/09/07 16:09:06 | - low match to Acid_4841 | |
LUAcid_KM3_B4_19 | 30556 | 29645 | | | on Willebrand factor, type A | | 1 | R | ADDED | | | | - best match to Solibacter usitatus Ellin6076 (30% id) - length OK - IPR002035 von Willebrand factor, type A family - general prediction only; very big family - no COG | PROTEIN | | | Good | AB | 82.227.62.180 | 15/09/07 16:14:18 | - several matches in both genomes | |
LUAcid_KM3_B4_18 | 29479 | 28742 | | | hypothetical protein | | 42 | R | ADDED | | | | - best match to formiate DH gamma subunit ( - very low COG hits Delftia acidovorans (28% ID) - start to 42, overlap and lenght to matches - | PROTEIN | | | Good | B | 82.227.62.180 | 15/09/07 16:20:58 | - no matches in genomes and clones | |
LUAcid_KM3_B4_17 | 28782 | 28534 | | | hypothetical protein (perhaps not a protein) | | 1 | R | ADDED | | | | - no match - no COG | PROTEIN | | | - | | 82.227.62.180 | 15/09/07 16:23:38 | - not match in genomes and clones | |
LUAcid_KM3_B4_16 | 27276 | 28727 | | | membrane bound O-acyl transferase, MBOAT family protein | | 1 | D | ADDED | | | | - best match to Rhodopseudomonas palustris (36% id) - also COG0057 - pfam03062, MBOAT, MBOAT family - lenght OK | PROTEIN | COG1696 Predicted membrane protein involved in D-alanine export | M Cell wall/membrane/envelope biogenesis | Good | B | 82.227.62.180 | 15/09/07 16:30:14 | - two matches in both genomes - no match in clones | |
LUAcid_KM3_B4_15 | 27038 | 26292 | | | coenzyme PQQ synthesis protein C | | 1 | R | ADDED | | | | - best match to Chlamydophila felis Fe/C-56 (39% id) - IPR004305 TENA/THI-4 protein: proteins containing this domain are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase | PROTEIN | COG5424 Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C | H Coenzyme transport and metabolism | Good | ABE | 82.227.62.180 | 15/09/07 16:35:21 | - single match to Acid345_0078 (38% id) in acidos | |
LUAcid_KM3_B4_14 | 24631 | 26178 | | | conserved hypothetical protein | | 1 | D | ADDED | | | | - best match to Acid_3771 - no COG - two types of proteins with similarities, but different in length (400 aa and 600aa) - similarities to different Planctomyces... - low match to cytochrom c region family IPR012282 Cytochrome c region | PROTEIN | | | Good | | 82.227.62.180 | 17/09/07 08:31:21 | - paralog in same clone KM3_25_B4_210 (53% id) - several orthologs in Solibacter but only one in Ellin6706 - similarity to Cytochrome c family ORF5 on aplysina clone pAPKS18 (Fieseler 2007) | |
LUAcid_KM3_B4_13 | 21602 | 24304 | | | - conserved outermembrane protein | | 44 | D | ADDED | | | | - best match to secreted protein Gramella forsetii (32% id) - best matches to CFB group bacteria - no COG - start codon to 44aa - low match to PR008960 Carbohydrate-binding family 9/cellobiose dehydrogenase, cytochrome - OMPA-like superfamily; transmembrane and subsurface protein family - DAS transmembrane prediction: 3 transmembrane regions --> from 86aa to 944 outside - secreted protein | PROTEIN | | | Good | B | 82.227.62.180 | 17/09/07 08:59:45 | - best match to Acid345_0818 (33% id) - no other matches in Acidobacteria - not on clones | |
LUAcid_KM3_B4_12 | 19754 | 21385 | | | Pyrrolo-quinoline quinone like protein | | 1 | D | ADDED | | | | - best match to Solibacter (46% id) - good match to IPR002372 Pyrrolo-quinoline quinone: Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases [1, 2]. A number of bacterial quinoproteins belong to this family. - Beta-propeller repeat occurring in enzymes with pyrrolo-quinoline quinone (PQQ) as cofactor, in Ire1p-like Ser/Thr kinases, and in prokaryotic dehydrogenases. - length OK | PROTEIN | COG4833 Predicted glycosyl hydrolase | G Carbohydrate transport and metabolism | Good | B | 82.227.62.180 | 17/09/07 09:12:36 | - several paralogs in Solibacter, best Acid_4577 (46% id) - no matches in other Acidobacteria - good match to uncultured bacterium 582 (Delong) | |
LUAcid_KM3_B4_11 | 18949 | 19734 | | | putative heme-binding protein | | 1 | D | ADDED | | | | - matches only to Solibacter (Acid_3123, 31% id, and 4576) with similar length - matches also to other proteins very much longer - no COG | PROTEIN | | | Good | unique | 82.227.62.180 | 17/09/07 09:23:06 | - conserved with adjacent outermembrane protein at least in Solibacter (2 times) and here | |
LUAcid_KM3_B4_10 | 18843 | 18328 | | | Cupin 2, conserved barrel protein | | 1 | R | ADDED | | | | - best match to Rubrobacter xylanophilus (43% id), but here approximately 40aa too long - length ? | PROTEIN | COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain | S Function unknown | Good | B | 82.227.62.180 | 17/09/07 09:30:51 | - low match to Acid_2912 which is longer | |
LUAcid_KM3_B4_09 | 16969 | 18207 | | | amidohydrolase family protein | | 1 | D | ADDED | | | | - best match to Mycobacterium smegmatis (29% id) - length OK - very big family: This group of enzymes represents a large metal dependent hydrolase superfamily - in B plus 2 matches in Aspergillus | PROTEIN | COG1228 Imidazolonepropionase and related amidohydrolases | Q Secondary metabolites biosynthesis, transport and catabolism | Good | B | 82.227.62.180 | 17/09/07 09:46:17 | - several matches to amidohydrolase in both genomes - not on other clones - enviironment not conserved | |
LUAcid_KM3_B4_08 | 15859 | 16857 | | | hypothetical protein | | 1 | D | ADDED | | | | - no matches - no COG | PROTEIN | | | Good | unique | 82.227.62.180 | 17/09/07 09:48:28 | | |
LUAcid_KM3_B4_07 | 14345 | 15859 | | | Cytochrome c domain protein | | 1 | D | ADDED | | | | - best match to putative thiol-disulfide isomerase or thioredoxin (Solibacter, 30% id) - no COG - several matches in Planctomycetes | PROTEIN | | | Good | BE | 82.227.62.180 | 17/09/07 09:59:34 | - paralog on clone: high similarity to KM3_25_B4_095 (54% id) - several matches in Solibacter, one match in Ellin6706 - environment on clone not conserved | |
LUAcid_KM3_B4_06 | 14127 | 13603 | | | hypothetical outermembrane protein | | 1 | R | ADDED | | | | - best match to probable secreted glycosyl hydrolase Planctomyces maris, (26% id), low similarity - no COG - one transmembrane domain - probable outermembrane protein - length OK | PROTEIN | | | Good | | 82.227.62.180 | 17/09/07 10:31:02 | - one low match to Acid_4894 protein of unknown function DUF44 - no match in other Acidobacteria | |
LUAcid_KM3_B4_05 | 12333 | 13586 | | | predicted transporter component | | 1 | D | ADDED | | | | - best match to COG2391: Predicted transporter component Burkholderia dolosa (58% id) - large family - IPR007272 Protein of unknown function DUF395, YeeE/YedE: transmembrane protein of unknown function - length OK | PROTEIN | COG2391 Predicted transporter component | R General function prediction only | Good | | 82.227.62.180 | 17/09/07 12:07:35 | - no hits to acidobacteria - environment not conserved | |
LUAcid_KM3_B4_04 | 10456 | 12318 | | | Pyrrolo-quinoline quinone (Quinoprotein alcohol dehydrogenase-like) | | 1 | D | ADDED | | | | - best match to Quinoprotein glucose dehydrogenase Solibacter usitatus Ellin6076 (42% id) | PROTEIN | COG4993 Glucose dehydrogenase | G Carbohydrate transport and metabolism | Good | B | 82.227.62.180 | 17/09/07 12:17:32 | - similarity on same clone KM3_25_B4_153 (29% id) and KM3_47_B8_099 (29% id) - high number of matches to Solibacter, not to Ellin6706 | |
LUAcid_KM3_B4_03 | 7883 | 10234 | | | glucose/sorbosone DH fused to 4-carboxymuconolactone decarboxylase domain protein | | 1 | D | ADDED | | | | - fused protein: glucose/sorbosone DH (Azoarcus, 43% id) fused to carboxymuconolactone decarboxylase (marine gamma proteobacterium, 35% id) - best match to predicted glucose/sorbosone dehydrogenase [Azoarcus sp. EbN1 (43% id) - also COG2128, function unknown (Carboxymuconolactone decarboxylase - eventually fusion of 3 proteins: pfam02627, CMD, Carboxymuconolactone decarboxylase family. Carboxymuconolactone decarb... 79934 No 0.007 pfam02627, CMD, Carboxymuconolactone decarboxylase family. Carboxymuconolactone decarboxylase (CMD) EC:4.1.1.44 is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway. In these bifunctional proteins CMD represents the C-terminal domain, pfam00561 represents the N-terminal domain.. | PROTEIN | COG2133 Glucose/sorbosone dehydrogenases | G Carbohydrate transport and metabolism | Good | unique | 82.227.62.180 | 17/09/07 13:15:46 | - matches in both acidobacterial genomes - not on other clones | |
LUAcid_KM3_B4_02 | 7206 | 7685 | | | RmlC-like cupin region protein | | 3 | D | ADDED | | | | - best match to Acid345_0092 (42%) - no COG - Cupin region; RmlC-like cupins: RmlC (dTDP (deoxythimodone diphosphates)-4-dehydrorhamnose 3,5-epimerase; EC:5.1.3.13) is a dTDP-sugar isomerase enzyme involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria [1]. RmlC is a dimer, each monomer being formed from two beta-sheets arranged in a beta-sandwich, where the substrate-binding site is located between the two sheets of both monomers. - start to 3aa (ATG) | PROTEIN | | | - | BE | 82.227.62.180 | 17/09/07 13:27:35 | - two matches to Acid345, but not Solibacter | |
LUAcid_KM3_B4_01 | 47 | 1267 | | | tyrosyl-tRNA synthetase | | 1 | D | ADDED | | 6.1.1.1 | | - best match to soil clone 23k22 (60% id) | PROTEIN | COG0162 Tyrosyl-tRNA synthetase | J Translation, ribosomal structure and biogenesis | Good | ABE | 82.227.62.180 | 21/09/07 09:15:22 | - matches in other clones - matches in soil clones - environment conserved in Acidobacteria? - to be verified | |
LUACID_KM3_B4_16SRNA | 1556 | 3121 | | | 16S ribosomal RNA | | 1 | D | ADDED | 16SrRNA | | | | RNA | | | - | | 129.175.105.75 | 29/10/07 17:52:59 | | |
LUACID_KM3_B4_23SRNA | 3742 | 6631 | | | 23S ribosomal RNA | | 1 | D | ADDED | 23SrRNA | | | | RNA | | | - | | 129.175.105.75 | 29/10/07 17:53:18 | | |
LUACID_KM3_B4_5SRNA | 6924 | 7048 | | | 5S ribosomal RNA | | 1 | D | ADDED | 5SrRNA | | | | RNA | | | - | | 129.175.105.75 | 29/10/07 17:53:37 | | |
LUACID_KM3_B4_TRNA1 | 3298 | 3371 | | | tRNA-Ile (GAT) | | 1 | D | ADDED | tRNA-Ile | | | | TRNA | | | - | | 129.175.105.75 | 29/10/07 17:54:30 | | |
LUACID_KM3_B4_TRNA2 | 3463 | 3535 | | | tRNA-Ala (TGC) | | 1 | D | ADDED | tRNA-Ala | | | | TRNA | | | - | | 129.175.105.75 | 29/10/07 17:55:05 | | |
LUACID_KM3_B4_11 | 18949 | 19734 | | | heme-binding protein | | 1 | D | ADDED | | | | - matches only to Solibacter (Acid_3123, 31% id, and 4576) with similar length - matches also to other proteins very much longer - no COG | PROTEIN | | | Good | unique | 82.227.62.180 | 07/11/07 12:05:47 | - conserved with adjacent outermembrane protein at least in Solibacter (2 times) and here | |
LUACID_KM3_B4_13 | 21602 | 24304 | | | conserved outermembrane protein | | 44 | D | ADDED | | | | - best match to secreted protein Gramella forsetii (32% id) - best matches to CFB group bacteria - no COG - start codon to 44aa - low match to PR008960 Carbohydrate-binding family 9/cellobiose dehydrogenase, cytochrome - OMPA-like superfamily; transmembrane and subsurface protein family - DAS itransmembrane predictioni: 3 transmembrane regions --> from 86aa to 944 outside - secreted protein | PROTEIN | | | Good | B (only bacteria) | 82.227.62.180 | 07/11/07 12:06:04 | - best match to Acid345_0818 (33% id) - no other matches in Acidobacteria - not on clones | |
LUACID_KM3_B4_14 | 24631 | 26178 | | | Cytochrom C domain protein | | 1 | D | ADDED | | | | - best match to Acid_3771 - no COG - two types of proteins with similarities, but different in length (400 aa and 600aa) - similarities to different Planctomyces... - low match to cytochrom c region family IPR012282 Cytochrome c region | PROTEIN | | | Good | | 82.227.62.180 | 07/11/07 12:55:33 | - paralog in same clone KM3_25_B4_210 (53% id) - several orthologs in Solibacter but only one in Ellin6706 - similarity to Cytochrome c family ORF5 on aplysina clone pAPKS18 (Fieseler 2007) | |
LUACID_KM3_B4_18 | 29479 | 28742 | | | cytochrome B556 subunit-like protein | | 42 | R | ADDED | | | | - best match to formiate DH gamma subunit ( - very low COG hits Delftia acidovorans (28% ID) - start to 42, overlap and lenght to matches - | PROTEIN | | | Good | B (only bacteria) | 82.227.62.180 | 07/11/07 13:54:23 | - no matches in genomes and clones | |
LUACID_KM3_B4_15 | 27038 | 26292 | | | TENA/THI-4 protein | | 1 | R | ADDED | | | | - best match to Chlamydophila felis Fe/C-56 (39% id) -coenzyme PQQ synthesis protein C - IPR004305 TENA/THI-4 protein: proteins containing this domain are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase | PROTEIN | COG5424 Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C | H Coenzyme transport and metabolism | Good | ABE | 82.227.62.180 | 07/11/07 13:58:27 | - single match to Acid345_0078 (38% id) in acidos | |
LUACID_KM3_B4_04 | 10456 | 12318 | | | Quinoprotein alcohol dehydrogenase-like | | 1 | D | ADDED | | | | - best match to Quinoprotein glucose dehydrogenase Solibacter usitatus Ellin6076 (42% id) | PROTEIN | COG4993 Glucose dehydrogenase | G Carbohydrate transport and metabolism | Good | B (only bacteria) | 82.227.62.180 | 07/11/07 14:12:15 | - similarity on same clone KM3_25_B4_153 (29% id) and KM3_47_B8_099 (29% id) - high number of matches to Solibacter, not to Ellin6706 |