Current Annotation for L35480_AD106_G4 23/11/17

namestartcoordendcoord**deintronstart1directionstatusgnecgpcctype1kognumkogglimmerdompatauth10/10/03 00:00:00More Comments 
                    10/10/03 00:00:00  
L35480_AD106_G4_05646364439  Membrane-associated lipoprotein involved in thiamine biosynthesis (ApbE family) 1RADDEDapbE ApbE-like lipoprotein PROTEINCOG1477 Membrane-associated lipoprotein involved in thiamine biosynthesisH Coenzyme transport and metabolism- 82.227.62.18010/09/07 21:09:32  
LUAcid_AD106_G4_172416324933  hypothetical protein 1DADDED  hypothetical proteinone single match in Ellin345PROTEIN  Good 82.227.62.18010/09/07 21:42:06  
luAcid_AD106_G4_16sRNA1771719275  rRNA 1DADDED16S   RNA    82.227.62.18010/09/07 21:44:17  
luAcid_AD106_G4_23sRNA2041523302  rRNA 1DADDED23S   RNA    82.227.62.18010/09/07 21:44:38  
LUAcid_AD106_G4_0432811785  NhaC Na+/H+ antiporter 1RADDEDnahC NahCbest matches with Shewanella speciesPROTEINCOG1757 Na+/H+ antiporterC Energy production and conversionGood 82.227.62.18010/09/07 22:34:09  
LUAcid_AD106_G4_0533724736  MiaB like protein tRNA modifiying enzyme 1DADDED  MiaB like protein- very conserved; best matches 23k22 and 41b15 acidobacterial soil clones and Ellin345PROTEINCOG0621 2-methylthioadenine synthetaseJ Translation, ribosomal structure and biogenesisGood 82.227.62.18010/09/07 22:44:16  
LUAcid_AD106_G4_0659784743  radical SAM domain protein 1RADDED  radical SAM domain protein- very conserved in bacteria - best match to acidobacterial soil clones 23k22 and 41b15 - conserved in tandem with MiaB like protein in AcidobacteriaPROTEINJ Translation, ribosomal structure and biogenesis Good 82.227.62.18010/09/07 22:51:55  
LUAcid_AD106_G4_0760397292  putative protease 1DADDED  putative proteaseconserved in acidobacterial soil clone 23k22 and 41b15 with two adjacent proteins (057, 071, 082)PROTEINCOG0612 Predicted Zn-dependent peptidasesR General function prediction onlyGood 82.227.62.18010/09/07 22:58:43  
LUAcid_AD106_G4_0120352  truncated hypothetical protein 1DADDED  hypothetical protein- best match to Aquifex - COG prediction suspectPROTEINCOG4659 Predicted NADH:ubiquinone oxidoreductase, subunit RnfGC Energy production and conversionGood but overlapping 129.175.112.25211/09/07 09:37:04  
LUAcid_AD106_G4_0874118238  beta-lactamase-like protein 1DADDED  putative metallo-beta-lactamase family protein PROTEINCOG1235 Metal-dependent hydrolases of the beta-lactamase superfamily IR General function prediction onlyGood 129.175.112.25211/09/07 09:44:21  
L35480_AD106_G4_05646364439    1RDELETED       - 129.175.105.7511/09/07 10:08:11  
L35480_AD106_G4_00226621  test 1RADDED   test-commentPROTEINCOG0122 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylaseL Replication, recombination and repair- 129.175.105.7511/09/07 13:32:43  
L35480_AD106_G4_00226621    1RDELETED       - 129.175.105.7511/09/07 16:59:13  
LUAcid_AD106_G4_038281835  ApbE-like lipoprotein 45DADDED   - one match in Solibacter usitatus Ellin7606, not in A. bacterium Ellin345 - matches only bacteria, not archaea, not eukarya - best match with 31% identities - start codon changed after alignment (TTG to ATG at 45aa)PROTEINCOG1477 Membrane-associated lipoprotein involved in thiamine biosynthesisH Coenzyme transport and metabolismGood 82.227.62.18011/09/07 18:46:02  
LUAcid_AD106_G4_02352828  hypothetical transmembrane protein 1DADDED   - no COG - very low similarities - best match Ralstonia Rsc0621 protein considering length and cooccurence in Ralstonia with ApbE-like protein as here - after TMHMM scan: prediction of 4 TMhelicesPROTEIN  Good 82.227.62.18011/09/07 20:08:29  
LUAcid_AD106_G4_0982459540  adenylosuccinate lyase (PurB) 1DADDED   - very conserved - best match to acidobacterial clone 41b15 and 23k22 and A. bacterium Ellin345 - enzyme in purine ribonucleotide biosynthesis - calalytic reaction: N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP - length very good - cooccurence with beta lactamase domain protein in Solibacter usitatus Ellin6076 - equally here with ORF094PROTEINCOG0015 Adenylosuccinate lyaseF Nucleotide transport and metabolismGood 82.227.62.18011/09/07 20:32:48  
LUAcid_AD106_G4_1095469782  phosphoribosylformylglycinamidine synthase I (PurS) 1DADDED   - best match acidobacterial soil clones 23k22 and 41b15 containing gene cluster for purine ribonucleotide biosynthesis - length OKPROTEINCOG1828 Phosphoribosylformylglycinamidine (FGAM) synthase, PurS componentF Nucleotide transport and metabolismGood 82.227.62.18011/09/07 20:39:37  
LUAcid_AD106_G4_11983910552  phosphoribosylformylglycinamidine synthase I (PurQ; FGAM synthase I) 1DADDED   - best match acidobacterial soil clone 41b15 and 23k22 - 70% identity to 41b15 PurQ - part of purin biosynthesis operon - length OKPROTEIN F Nucleotide transport and metabolismGood 82.227.62.18011/09/07 21:20:06  
LUAcid_AD106_G4_121046812798  phosphoribosylformylglycinamidine synthase II (PurL) 31DADDED   - best match to acidobacterial soil clone 23k22 and 41b15 - FGAM Synthase II - in purin biosynthesis operon - change of start codon to 31 (ATG)PROTEINCOG0046 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domainF Nucleotide transport and metabolismGood 82.227.62.18011/09/07 21:25:32  
LUAcid_AD106_G4_131279814249  amidophosphoribosyl transferase (PurF) 4DADDED   - best match to acidobacterial soil clone 41b15 and 23k22 - purin biosynthesis operon - very conserved: 65% identity to PurF from 41b15 - change start codon to 4aa (ATG)PROTEINCOG0034 Glutamine phosphoribosylpyrophosphate amidotransferaseF Nucleotide transport and metabolismGood 82.227.62.18011/09/07 21:32:47  
LUAcid_AD106_G4_141430415395  phosphoribosylformylglycinamidine cyclo ligase (PurM, AIR Synthetase) 1DADDED   - best match to acidobacterial soil clones 23k22 and 41b15 - very conserved 63% identity to PurM of 23k22 - purin biosynthesis operon - PurM (Aminoimidazole Ribonucleotide [AIR] synthetasePROTEINCOG0150 Phosphoribosylaminoimidazole (AIR) synthetaseF Nucleotide transport and metabolismGood but overlapping 82.227.62.18011/09/07 21:37:59  
LUAcid_AD106_G4_151545616067  phosphoribosylglycinamide formyltransferase (PurN) 8DADDED   - best match to acidobacterial soil clones 23k22 and 41b15 - purin biosynthesis operon - very conserved: 62% identiy - folate dependent enzyme - start codon change to 8aa (ATG), since first 10aa not conserved, choose of ATG instead of GTGPROTEINCOG0299 Folate-dependent phosphoribosylglycinamide formyltransferase PurNF Nucleotide transport and metabolismGood 82.227.62.18011/09/07 21:50:56  
LUAcid_AD106_G4_161606717302  tyrosyl-tRNA synthetase (TyrS) 8DADDED   - best match acidobacterial soil clone 23k22, then Solibacter and proteobacteria - very conserved: 52% identity to 23k22 - eventually phylogeny - change of start codon to 8aa, since overlap and comparison to other TyrSPROTEINCOG0162 Tyrosyl-tRNA synthetaseJ Translation, ribosomal structure and biogenesisGood 82.227.62.18012/09/07 08:29:06  
LUAcid_AD106_G4_182515726686  conserved hypothetical protein 1DADDED   - best match to Myxococcus xanthus 7198 - also good match to Ellin345 (ORF Acid2212) and Solibacter (Ellin 6706) ORF 2212 - homologs annotated as putative lipoprotein ? - InterPro: zinc metallopeptidase domain - no transmembrane domain - no COG hit - start codon OKPROTEIN  Good 82.227.62.18012/09/07 09:14:59  
LUAcid_AD106_G4_192670028145  FAD linked oxidase 12DADDED   - best match Rubrobacter xylanophilus - very conserved 56% identity - D-lactat dehydrogenase (cytochrome) - FAD/FMN- containing dehydrogenase (GlcD) - start codon change to 12aa, to eluminate overlap and change from TTG to ATGPROTEINCOG0277 FAD/FMN-containing dehydrogenasesC Energy production and conversionGood 82.227.62.18012/09/07 16:23:11  
LUAcid_AD106_G4_202816729429  FAD linked oxidase-like protein (GlcE subunit ?) 1DADDED   - best match to Rubrobacter xylanophilus (YP_645556.1) - very conserved 40% identity - together with 331 (best match to YP_645557.1) and 348 seems to be two subunits of Glycolate oxidase - ORF348 subunit GlcE - ORF 331 and 348 in tandem also in RubrobacterPROTEINEnergy Good 82.227.62.18012/09/07 16:36:45  
LUAcid_AD106_G4_213083429509  protein of unknown function DUF224 1RADDED    PROTEIN  Good 82.227.62.18012/09/07 17:47:25  
LUAcid_AD106_G4_213083429509  protein of unknown function DUF224 1RADDED   - best match to Rubrobacter xylanophilus (Actinobacteria high GC gram+) (YP_645555.1) (Glycolate oxidase subunit GlcF?) - very conserved 58% identity - together with 331 (best match to YP_645557.1) and 348 (YP_645556.1) seems to be three subunits of Glycolate oxidase - ORF348 subunit GlcE - ORF 331 and 348 and 363 also in Rubrobacter - match also in Solibacter, but low e-value, seems to be another protein - in general matches in all kind of bacteria PROTEIN  Good 82.227.62.18012/09/07 17:48:06  
LUAcid_AD106_G4_223100532000  NADPH:quinone reductase and related Zn-dependent oxidoreductases 1DADDED   - best match to Magnetospirillum magneticum ZP_00054546 - very conserved 56% identity - not present in soil clones - present in sequnces acidobacteriaPROTEINCOG0604 NADPH:quinone reductase and related Zn-dependent oxidoreductasesC Energy production and conversionGood 82.227.62.18012/09/07 18:06:30  
LUAcid_AD106_G4_233202332481  Endoribonuclease L-PSP 35DADDED   - best match to Ellin345 YP_593389.1 - change of start codon to 35aa - Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3] - could be involved in purin biosynthesisPROTEINCOG0024 Methionine aminopeptidaseJ Translation, ribosomal structure and biogenesisGood 82.227.62.18012/09/07 18:16:08  
LUAcid_AD106_G4_243249234354  gamma-glutamyltranspeptidase 1DADDED   - best match to Congregibacter litoralis KT71 - very conserved 53% identity - 7 homologs in Ellin345 - Gamma-glutamyltranspeptidase (GGT) catalyses the transfer of the glutathione gamma-glutamyl moiety to an acceptor that may be an amino acid, a peptide or water (forming glutamate) [1]. GGT plays a central role in glutathione metabolism, and drug and xenobiotic detoxification [2]. In both prokaryotes and eukaryotes, the enzyme contains heavy and light subunits, which are processed from a single chain precursor. The light subunit houses the GGT active site.PROTEIN  Good 82.227.62.18012/09/07 18:41:29  
LUAcid_AD106_G4_253436034848  acetyltransferase (GNAT) family protein 4DADDED   - best match to Desulfovibrio desulfuricans G20 - 39% identity - start codon changed to 4aa in accordance to length of homologs; but start codon also at 12aaPROTEINCOG0454 Histone acetyltransferase HPA2 and related acetyltransferasesK TranscriptionGood 82.227.62.18012/09/07 18:48:39  
LUAcid_AD106_G4_263533534865  hypothetical protein 11RADDED   - best match to Salinibacter ruber - 32% identity - change of start codon to 11aaPROTEIN  Good 82.227.62.18012/09/07 18:52:19  
LUAcid_AD106_G4_293627237018  protein of unknown function DUF28 1DADDED   - best matches to both Acidobacteria (Ellin345_2125); Ellin6706: Acid5948; 56% identity - present in clone KM3_47_B8_048 (ORF048) - more than 73% identity - conserved in all Bacteria, not in Archaea and EukaryaPROTEINCOG0217 Uncharacterized conserved proteinS Function unknownGood 82.227.62.18013/09/07 08:21:01  
LUAcid_AD106_G4_303701837569  crossover junction endodeoxyribonuclease RuvC 1DADDED   - conserved region in two clones KM3_47_B8 and AD106_G4, DUF28, RuvC (Holliday junction nuclease), RuvA (Holliday junction ATP-dependent DNA helicase ruvA), RuvB (Holliday junction ATP-dependent DNA helicase ruvB) - syntheny conserved in other Bacteria with DUF28 - present in clone KM3_47_B8_039 (ORF39), region conserved (operon?) with DUF0028 and KM3_47_B8_032 (ORF32) and KM3_47_B8_026 (ORF26), same as here with ORF452 (Holliday junction DNA helicase RuvA) and ORF467 RuvB - best match to Ellin345_3618; 48%identity and to clone KM3_47_B8_39; 57% identity PROTEINCOG0817 Holliday junction resolvasome, endonuclease subunitL Replication, recombination and repair- 82.227.62.18013/09/07 09:23:07  
LUAcid_AD106_G4_313757538174  Holliday junction DNA helicase RuvA 1DADDED   - conserved region in two clones KM3_47_B8 and AD106_G4, DUF28, RuvC (Holliday junction nuclease), RuvA (Holliday junction ATP-dependent DNA helicase ruvA), RuvB (Holliday junction ATP-dependent DNA helicase ruvB) PROTEINCOG0632 Holliday junction resolvasome, DNA-binding subunitL Replication, recombination and repairGood 82.227.62.18013/09/07 09:39:27  
LUAcid_AD106_G4_323818339199  Holliday junction DNA helicase RuvB 1DADDED   - best match to Acid_4544 58% identity and Acid_0957 - match also to KM3_47_B8_026, but sequence in this clone very short, must be verifiedPROTEINCOG2255 Holliday junction resolvasome, helicase subunitL Replication, recombination and repairGood 82.227.62.18013/09/07 09:47:56  
LUAcid_AD106_G4_333932140307  3-oxoacyl-(acyl-carrier-protein) synthase III 15DADDED   - best match Solibacter usitatus Ellin6076 Acid_7048 and Ellin345 Acid345_2017, 61% identities - not in other clonesPROTEINCOG0332 3-oxoacyl-[acyl-carrier-protein] synthase IIII Lipid transport and metabolismGood 82.227.62.18013/09/07 10:17:09  
LUAcid_AD106_G4_344035041399  S-adenosylmethionine:tRNA ribosyltransferase-isomerase 1DADDED   - best match Geobacillus 48% identity - very conserved in Bacteria, not in A and E - not in other clones - lower matches in Ellin345 and Ellin6706PROTEINCOG0809 S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase)J Translation, ribosomal structure and biogenesisGood 82.227.62.18013/09/07 10:25:22  
LUAcid_AD106_G4_273538635817  hypothetical protein 20DADDED   - SAM binding motif - Methyltransferase type 11 motif - but low similarity - change of start codon to 20aa because of overlapPROTEIN  Good 82.227.62.18013/09/07 10:30:15  
LUAcid_AD106_G4_283581336151  hypothetical protein 1DADDED   - very low similarity - length not corresponding - InterPro: Methyltransferase as ORF430 perhaps frameshift and 430+433 corresponds to one genePROTEIN  Good 82.227.62.18013/09/07 11:02:42  
LUAcid_AD106_G4_354182841487  hypothetical protein 1RADDED   - low similarity - domain: Ribonuclease H-like - but ORF too short - transposase similarity - integrase, calatytic region match - helix-turn-helix Fis type matchPROTEIN  - 82.227.62.18013/09/07 11:12:05  
L35480_AD106_G4_00226621    1RDELETED       - 129.175.105.7513/09/07 18:45:09  
LUAcid_AD106_G4_0874118238  beta-lactamase-like protein 1DADDED   - Clostridium thermocellum ATCC 27405 (36% id) - also COG0324 - seems to be part of purin operonPROTEINCOG1235 Metal-dependent hydrolases of the beta-lactamase superfamily IR General function prediction onlyGood 82.227.62.18018/09/07 09:20:37- 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_AD106_G4_0982459540  adenylosuccinate lyase (PurB) 1DADDED   - best match to KM3_187_G1_032 (68% id) - next match 23k22 (65% id) - purine ribonucleotide biosynthetic processPROTEINCOG0015 Adenylosuccinate lyaseF Nucleotide transport and metabolismGoodABE82.227.62.18018/09/07 11:30:22- 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_AD106_G4_1095469782  phosphoribosylformylglycinamidine synthase I (PurS) 1DADDED   - best match to KM3_205_D9_268 (70% id) - purin biosynthesis pathwayPROTEINCOG1828 Phosphoribosylformylglycinamidine (FGAM) synthase, PurS componentF Nucleotide transport and metabolismGoodAB82.227.62.18018/09/07 11:46:31- 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_AD106_G4_11983910552  phosphoribosylformylglycinamidine synthase I (PurQ) 1DADDED   best match to KM3_205_D9_262 (84% id) - Purin biosynthesis operonPROTEINCOG0047 Phosphoribosylformylglycinamidine (FGAM) synthase, glutamine amidotransferase domainF Nucleotide transport and metabolismGoodAB82.227.62.18018/09/07 13:08:57- 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_AD106_G4_121046812798  phosphoribosylformylglycinamidine synthase II (PurL) 1DADDED 6.3.5.3 best match to KM3_205_D9_254 (77% 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.PROTEINCOG0046 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domainF Nucleotide transport and metabolismGoodAB82.227.62.18018/09/07 13:58:19several 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_AD106_G4_131279814249  amidophosphoribosyl transferase (PurF) 1DADDED 2.4.2.14 - best match to KM3_205_D9_226 (78% 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].PROTEINCOG0034 Glutamine phosphoribosylpyrophosphate amidotransferaseF Nucleotide transport and metabolismGoodABE82.227.62.18018/09/07 16:23:38several 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_AD106_G4_0120352  truncated hypothetical protein 1DADDED  hypothetical protein- best match to Aquifex - COG prediction suspectPROTEINCOG4659 Predicted NADH:ubiquinone oxidoreductase, subunit RnfGC Energy production and conversionGood but overlapping 82.227.62.18001/10/07 11:15:31- good partial match to KM3_205_D9_412 and 373 - doimain pattern: B 
LUACID_AD106_G4_172416324933  hypothetical protein 1DADDED  hypothetical proteinone single match in Ellin345PROTEIN  Good 82.227.62.18008/10/07 15:26:15conserved only in deep sea acidobacterial clones: AD106_G4_17 KM3_A5_18 KM3_D9_23 KM3_G1_12 KM3_B8D2_15 Acid345_1727, not Solibacter - overall identity with 6 sequences >40% --> very conserved - domain pattern - unique for deep sea 
LUACID_AD106_G4_182515726686  conserved hypothetical protein 1DADDED   - best match to Myxococcus xanthus 7198 - also good match to Ellin345 (ORF Acid2212) and Solibacter (Ellin 6706) ORF 2212 - homologs annotated as putative lipoprotein ? - InterPro: zinc metallopeptidase domain - no transmembrane domain - no COG hit - start codon OKPROTEIN  Good 82.227.62.18008/10/07 15:39:14- very conserved in acidobacteria; 5 matches in deep sea clones, no matches in soil clones, one match in each genome, matches also in other bacteria AD106_G4_18 KM3_G1_13 KM3_D9_25 KM3_B8D2_17 KM3_A5_19 ACID345_3935 ACID_2212  
LUACID_AD106_G4_16SRNA1771719275  16S ribosomal RNA 1DADDED16SrRNA   RNA    129.175.105.7529/10/07 17:21:32  
LUACID_AD106_G4_23SRNA2041523302  23S ribosomal RNA 1DADDED23SrRNA   RNA    129.175.105.7529/10/07 17:22:33  
LUACID_AD106_G4_5SRNA2365023774  5S ribosomal RNA 1DADDED5SrRNA   RNA    129.175.105.7529/10/07 17:23:44  
LUACID_AD106_G4_TRNA11952019593  tRNA-Ile (GAT) 1DADDEDtRNA-Ile   TRNA    129.175.105.7529/10/07 17:26:27  
LUACID_AD106_G4_TRNA22000920081  tRNA-Ala (TGC) 1DADDEDtRNA-Ala   TRNA    129.175.105.7529/10/07 17:27:07  
LUACID_AD106_G4_TRNA34144241515  tRNA-Met (CAT) 1DADDEDtRNA-Met   TRNA    129.175.105.7529/10/07 17:28:00  
LUACID_AD106_G4_0659784743  radical SAM domain protein 1RADDED   - very conserved in bacteria - best match to acidobacterial soil clones 23k22 and 41b15 - conserved in tandem with MiaB like protein in AcidobacteriaPROTEINCOG0820 Predicted Fe-S-cluster redox enzymeR General function prediction onlyGoodB129.175.105.7517/12/07 14:37:25fixed COG -yz 
LUACID_AD106_G4_213083429509  Glycolate oxidase, iron-sulphur subunit 1RADDEDglcF  - best match to Rubrobacter xylanophilus (Actinobacteria high GC gram+) (YP_645555.1) (Glycolate oxidase subunit GlcF?) - very conserved 58% identity - together with 331 (best match to YP_645557.1) and 348 (YP_645556.1) seems to be three subunits of Glycolate oxidase - ORF348 subunit GlcE - ORF 331 and 348 and 363 also in Rubrobacter - match also in Solibacter, but low e-value, seems to be another protein - in general matches in all kind of bacteriaPROTEINCOG0247 Fe-S oxidoreductaseC Energy production and conversionGoodB129.175.105.7517/12/07 14:53:57fixed def/cog/gN -yz 
LUACID_AD106_G4_243249234354  gamma-glutamyltranspeptidase 1DADDEDggt2.3.2.2 - best match to Congregibacter litoralis KT71 - very conserved 53% identity - 7 homologs in Ellin345 - Gamma-glutamyltranspeptidase (GGT) catalyses the transfer of the glutathione gamma-glutamyl moiety to an acceptor that may be an amino acid, a peptide or water (forming glutamate) [1]. GGT plays a central role in glutathione metabolism, and drug and xenobiotic detoxification [2]. In both prokaryotes and eukaryotes, the enzyme contains heavy and light subunits, which are processed from a single chain precursor. The light subunit houses the GGT active site.PROTEINCOG0405 Gamma-glutamyltransferaseE Amino acid transport and metabolismGood 129.175.105.7517/12/07 15:09:10fixed EC/gN/COG -yz 
LUACID_AD106_G4_354182841487  hypothetical protein 1RADDED   - low similarity - domain: Ribonuclease H-like - but ORF too short - transposase similarity - integrase, calatytic region match - helix-turn-helix Fis type matchPROTEINCOG2801 Transposase and inactivated derivativesL Replication, recombination and repair- 129.175.105.7517/12/07 15:59:31  
LUACID_AD106_G4_0120352  truncated hypothetical protein 1DADDED   - best match to Aquifex - COG prediction suspectPROTEIN  Good but overlapping 129.175.105.7517/12/07 17:17:51fixed COG -yz 
LUACID_AD106_G4_0533724736  MiaB like protein tRNA modifiying enzyme 1DADDEDMiaB-like  - very conserved; best matches 23k22 and 41b15 acidobacterial soil clones and Ellin345PROTEINCOG0621 2-methylthioadenine synthetaseJ Translation, ribosomal structure and biogenesisGood 129.175.105.7530/01/08 17:19:09  
LUACID_AD106_G4_0982459540  adenylosuccinate lyase (PurB) 1DADDEDPurB  - best match to KM3_187_G1_032 (68% id) - next match 23k22 (65% id) - purine ribonucleotide biosynthetic processPROTEINCOG0015 Adenylosuccinate lyaseF Nucleotide transport and metabolismGoodABE129.175.105.7530/01/08 17:33:39- 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_AD106_G4_1095469782  phosphoribosylformylglycinamidine synthase I (PurS) 1DADDEDPurS  - best match to KM3_205_D9_268 (70% id) - purin biosynthesis pathwayPROTEINCOG1828 Phosphoribosylformylglycinamidine (FGAM) synthase, PurS componentF Nucleotide transport and metabolismGoodAB129.175.105.7530/01/08 17:35:18- 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_AD106_G4_11983910552  phosphoribosylformylglycinamidine synthase I (PurQ) 1DADDEDPurQ  best match to KM3_205_D9_262 (84% id) - Purin biosynthesis operonPROTEINCOG0047 Phosphoribosylformylglycinamidine (FGAM) synthase, glutamine amidotransferase domainF Nucleotide transport and metabolismGoodAB129.175.105.7530/01/08 17:36:07- 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_AD106_G4_121055812798  phosphoribosylformylglycinamidine synthase II (PurL) 1DADDEDPurL6.3.5.3 best match to KM3_205_D9_254 (77% id) - purin biosynthesis operon - AIR synthase related protein - Ġde novoĠ 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.PROTEINCOG0046 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domainF Nucleotide transport and metabolismGoodAB129.175.105.7530/01/08 17:37:12several 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_AD106_G4_131280714249  amidophosphoribosyl transferase (PurF) 1DADDEDPurF2.4.2.14 - best match to KM3_205_D9_226 (78% 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].PROTEINCOG0034 Glutamine phosphoribosylpyrophosphate amidotransferaseF Nucleotide transport and metabolismGoodABE129.175.105.7530/01/08 17:39:54several 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_AD106_G4_141430415395  phosphoribosylformylglycinamidine cyclo ligase (PurM, AIR Synthetase) 1DADDEDPurM  - best match to acidobacterial soil clones 23k22 and 41b15 - very conserved 63% identity to PurM of 23k22 - purin biosynthesis operon - PurM (Aminoimidazole Ribonucleotide [AIR] synthetasePROTEINCOG0150 Phosphoribosylaminoimidazole (AIR) synthetaseF Nucleotide transport and metabolismGood but overlapping 129.175.105.7530/01/08 17:41:58  
LUACID_AD106_G4_151545616067  phosphoribosylglycinamide formyltransferase (PurN) 8DADDEDPurN  - best match to acidobacterial soil clones 23k22 and 41b15 - purin biosynthesis operon - very conserved: 62% identiy - folate dependent enzyme - start codon change to 8aa (ATG), since first 10aa not conserved, choose of ATG instead of GTGPROTEINCOG0299 Folate-dependent phosphoribosylglycinamide formyltransferase PurNF Nucleotide transport and metabolismGood 129.175.105.7530/01/08 17:42:24  
LUACID_AD106_G4_161606717302  tyrosyl-tRNA synthetase (TyrS) 8DADDEDTyrS  - best match acidobacterial soil clone 23k22, then Solibacter and proteobacteria - very conserved: 52% identity to 23k22 - eventually phylogeny - change of start codon to 8aa, since overlap and comparison to other TyrSPROTEINCOG0162 Tyrosyl-tRNA synthetaseJ Translation, ribosomal structure and biogenesisGood 129.175.105.7530/01/08 17:42:47  
LUACID_AD106_G4_303701837569  crossover junction endodeoxyribonuclease RuvC 1DADDEDRuvC  - conserved region in two clones KM3_47_B8 and AD106_G4, DUF28, RuvC (Holliday junction nuclease), RuvA (Holliday junction ATP-dependent DNA helicase ruvA), RuvB (Holliday junction ATP-dependent DNA helicase ruvB) - syntheny conserved in other Bacteria with DUF28 - present in clone KM3_47_B8_039 (ORF39), region conserved (operon?) with DUF0028 and KM3_47_B8_032 (ORF32) and KM3_47_B8_026 (ORF26), same as here with ORF452 (Holliday junction DNA helicase RuvA) and ORF467 RuvB - best match to Ellin345_3618; 48%identity and to clone KM3_47_B8_39; 57% identityPROTEINCOG0817 Holliday junction resolvasome, endonuclease subunitL Replication, recombination and repair- 129.175.105.7530/01/08 17:43:29  
LUACID_AD106_G4_313757538174  Holliday junction DNA helicase RuvA 1DADDEDRuvA  - conserved region in two clones KM3_47_B8 and AD106_G4, DUF28, RuvC (Holliday junction nuclease), RuvA (Holliday junction ATP-dependent DNA helicase ruvA), RuvB (Holliday junction ATP-dependent DNA helicase ruvB)PROTEINCOG0632 Holliday junction resolvasome, DNA-binding subunitL Replication, recombination and repairGood 129.175.105.7530/01/08 17:43:59  
LUACID_AD106_G4_323818339199  Holliday junction DNA helicase RuvB 1DADDEDRuvB  - best match to Acid_4544 58% identity and Acid_0957 - match also to KM3_47_B8_026, but sequence in this clone very short, must be verifiedPROTEINCOG2255 Holliday junction resolvasome, helicase subunitL Replication, recombination and repairGood 129.175.105.7530/01/08 17:44:22