GapMind for catabolism of small carbon sources

 

L-asparagine catabolism

Analysis of pathway asparagine in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 ans, BPHYT_RS17540
Acidithiobacillus ferrooxidans ATCC 23270 ans, BPHYT_RS17540
Acidovorax sp. GW101-3H11 ans, aatJ, aatQ, aatM, aatP
Algiphilus aromaticivorans DG1253 ans, dauA
Alicycliphilus denitrificans K601 ans, aatJ, aatQ, aatM, aatP
Alkalihalobacterium alkalinitrilicum DSM 22532 ans, glt
Allochromatium vinosum DSM 180 ans, glt
Ammonifex degensii KC4 ans, glt
Anaerobutyricum hallii DSM 3353 ans, glt
Aquimarina longa SW024 ans, glt
Archaeoglobus veneficus SNP6 ans, glt
Arcobacter nitrofigilis DSM 7299 ans, glt
Azoarcus olearius BH72 ans, aatJ, aatQ, aatM, aatP
Azohydromonas australica DSM 1124 ans, aatJ, aatQ, aatM, aatP
Azorhizobium caulinodans ORS 571 ans, aatJ, aatQ, aatM, aatP
Azospirillum brasilense Sp245 bztA, bztB, bztC, bztD, ans
Azospirillum sp. B510 ans, glt
Bacteroides thetaiotaomicron VPI-5482 yhiT, ans
Beijerinckia indica ATCC 9039 ans, aapJ, aapQ, aapM, aapP
Beijerinckia mobilis UQM 1969 ans, aapJ, aapQ, aapM, aapP
Billgrantia desiderata SP1 ans, dauA
Bradyrhizobium sp. BTAi1 aapJ, aapQ, aapM, aapP, ans
Brevundimonas sp. GW460-12-10-14-LB2 ans, glt
Burkholderia phytofirmans PsJN ans, aatJ, aatQ, aatM, aatP
Burkholderia vietnamiensis G4 ans, aatJ, aatQ, aatM, aatP
Calditerrivibrio nitroreducens DSM 19672 ans, dauA
Caminibacter mediatlanticus TB-2 ans, glt
Carboxydothermus pertinax Ug1 ans, glt
Caulobacter crescentus NA1000 ans, glt
Cereibacter sphaeroides ATCC 17029 ans, bztA, bztB, bztC, bztD
Chlorobaculum parvum NCIB 8327 ans, dauA
Chlorobaculum tepidum TLS ans, dauA
Chlorobium limicola DSM 245 ans, dauA
Chlorobium phaeobacteroides BS1 ans, glt
Clostridium acetobutylicum ATCC 824 ans, glt
Clostridium kluyveri DSM 555 agcS, ans
Clostridium tyrobutyricum FAM22553 ans, glt
Crocosphaera subtropica ATCC 51142 ans, natF, bgtB', natH, bgtA
Cupriavidus basilensis FW507-4G11 ans, aatJ, aatQ, aatM, aatP
Dechloromonas agitata is5 ans, glt
Dechlorosoma suillum PS ans, aatJ, aatQ, aatM, aatP
Dehalococcoides mccartyi 195 ans, glt
Denitrovibrio acetiphilus DSM 12809 yhiT, ans
Derxia gummosa DSM 723 ans, aatJ, aatQ, aatM, aatP
Desulfacinum hydrothermale DSM 13146 ans, aapJ, aapQ, aapM, aapP
Desulfacinum infernum DSM 9756 ans, aapJ, aapQ, aapM, aapP
Desulfarculus baarsii DSM 2075 ans, glt
Desulfatibacillum aliphaticivorans DSM 15576 ans, glt
Desulfatiglans anilini DSM 4660 ans, glt
Desulfitobacterium hafniense DCB-2 ansP, ans
Desulfobacca acetoxidans DSM 11109 ans, glt
Desulfobacter vibrioformis DSM 8776 ans, glt
Desulfogranum mediterraneum DSM 13871 ans, dauA
Desulforamulus ruminis DSM 2154 ans, glt
Desulfoscipio geothermicus DSM 3669 glnQ, glnP, ans
Desulfotalea psychrophila LSv54 ans, glt
Desulfovibrio oxyclinae DSM 11498 ans, glt
Desulfovibrio vulgaris Hildenborough JW710 ans, dauA
Desulfovibrio vulgaris Miyazaki F ans, dauA
Desulfurobacterium atlanticum DSM 15668 ans, glt
Desulfuromonas acetexigens yhiT, ans
Desulfuromusa kysingii DSM 7343 yhiT, ans
Dinoroseobacter shibae DFL-12 ans, bztA, bztB, bztC, bztD
Dyella japonica UNC79MFTsu3.2 ans, BPHYT_RS17540
Echinicola vietnamensis KMM 6221, DSM 17526 ans, glt
Escherichia coli BW25113 ans, aatJ, aatQ, aatM, aatP
Ferroglobus placidus DSM 10642 ans, glt
Frankia alni ACN14a ans, glt
Geobacter metallireducens GS-15 ans, glt
Geotalea uraniireducens Rf4 ans, glt
Halococcus hamelinensis 100A6 ans, glt
Haloechinothrix alba DSM 45207 agcS, ans
Haloferax volcanii DS2 ans, glt
Haloglycomyces albus DSM 45210 ans, glt
Halorhodospira halophila SL1 agcS, ans
Heliomicrobium modesticaldum Ice1; ATCC 51547 agcS, ans
Herbaspirillum autotrophicum IAM 14942 ans, aatJ, aatQ, aatM, aatP
Herbaspirillum seropedicae SmR1 ans, aatJ, aatQ, aatM, aatP
Hippea alviniae EP5-r ans, glt
Hydrogenophaga taeniospiralis NBRC 102512 ans, aatJ, aatQ, aatM, aatP
Hydrogenovibrio halophilus DSM 15072 ans, glt
Hydrogenovibrio kuenenii DSM 12350 ans, dauA
Hydrogenovibrio marinus DSM 11271 ans, dauA
Hyphomicrobium sulfonivorans WDL6 ans, glt
Klebsiella michiganensis M5al ans, aatJ, aatQ, aatM, aatP
Klebsiella variicola At-22 ans, aatJ, aatQ, aatM, aatP
Kyrpidia tusciae DSM 2912 ansP, ans
Leptospirillum ferrooxidans C2-3 ans, glt
Magnetospirillum magneticum AMB-1 ans, dauA
Malonomonas rubra DSM 5091 ans, aapJ, aapQ, aapM, aapP
Maridesulfovibrio bastinii DSM 16055 ans, aapJ, aapQ, aapM, aapP
Maridesulfovibrio zosterae DSM 11974 ans, aapJ, aapQ, aapM, aapP
Marinobacter adhaerens HP15 ans, glt
Mesorhizobium ciceri WSM1271 ans, aapJ, aapQ, aapM, aapP
Methanobacterium lacus AL-21 ans, glt
Methanococcus aeolicus Nankai-3 ans, glt
Methanococcus maripaludis C5 ans, dauA
Methanosarcina acetivorans C2A ans, glt
Methanosarcina mazei Go1 ans, glt
Methanospirillum lacunae Ki8-1 ans, glt
Methanothermobacter thermautotrophicus Delta H ans, glt
Methylobacterium nodulans ORS 2060 ans, aatJ, aatQ, aatM, aatP
Methylobacterium sp. 4-46 Apr-46 ans, aatJ, aatQ, aatM, aatP
Methylocapsa acidiphila B2 ans, aapJ, aapQ, aapM, aapP
Methylocapsa aurea KYG ans, aapJ, aapQ, aapM, aapP
Methylocella silvestris BL2 ans, dauA
Methylococcus capsulatus Bath ans, glt
Methylocystis bryophila S285 ans, glt
Methyloferula stellata AR4T ans, glt
Methylohalobius crimeensis 10Ki ans, glt
Methylomonas methanica MC09 agcS, ans
Methylosarcina fibrata AML-C10 agcS, ans
Methylotuvimicrobium alcaliphilum 20Z ans, glt
Methylovulum miyakonense HT12 ans, glt
Mycolicibacterium vanbaalenii PYR-1 ans, glt
Nitratifractor salsuginis DSM 16511 ans, glt
Nitratiruptor tergarcus DSM 16512 ans, glt
Nitriliruptor alkaliphilus DSM 45188 ans, dauA
Nocardioides dokdonensis FR1436 ans, glt
Nocardiopsis lucentensis DSM 44048 ans, glt
Nostoc punctiforme ATCC 29133; PCC 73102 ans, glt
Novosphingobium aromaticivorans DSM 12444 ans, glt
Oleispira antarctica ans, glt
Paraburkholderia atlantica CCGE1002 ans, aatJ, aatQ, aatM, aatP
Paraburkholderia bryophila 376MFSha3.1 ans, aatJ, aatQ, aatM, aatP
Paraburkholderia phymatum STM815 ans, aatJ, aatQ, aatM, aatP
Paucidesulfovibrio gracilis DSM 16080 ans, glt
Pedobacter sp. GW460-11-11-14-LB5 ans, glt
Pelobacter propionicus DSM 2379 ans, SLC7A13
Persephonella marina EX-H1 ans, glt
Phaeacidiphilus oryzae TH49 ans, BPHYT_RS17540
Phaeobacter inhibens BS107 ans, bztA, bztB, bztC, bztD
Polaromonas naphthalenivorans CJ2 ans, glt
Prosthecochloris aestuarii DSM 271 ans, glt
Pseudarthrobacter sulfonivorans Ar51 ans, glt
Pseudomonas benzenivorans DSM 8628 ans, aatJ, aatQ, aatM, aatP
Pseudomonas fluorescens FW300-N1B4 ans, aatJ, aatQ, aatM, aatP
Pseudomonas fluorescens FW300-N2C3 ans, aatJ, aatQ, aatM, aatP
Pseudomonas fluorescens FW300-N2E2 ans, aatJ, aatQ, aatM, aatP
Pseudomonas fluorescens FW300-N2E3 ans, aatJ, aatQ, aatM, aatP
Pseudomonas fluorescens GW456-L13 ans, aatJ, aatQ, aatM, aatP
Pseudomonas putida KT2440 ans, aatJ, aatQ, aatM, aatP
Pseudomonas simiae WCS417 ans, aatJ, aatQ, aatM, aatP
Pseudomonas stutzeri RCH2 ans, glt
Pyrolobus fumarii 1A ans, glt
Rhizobium etli CFN 42 ans, aapJ, aapQ, aapM, aapP
Rhizobium johnstonii 3841 ans, aapJ, aapQ, aapM, aapP
Rhizobium leguminosarum WSM1325 ans, aapJ, aapQ, aapM, aapP
Rhizorhabdus wittichii RW1 ans, glt
Rhodanobacter denitrificans FW104-10B01 ans, BPHYT_RS17540
Rhodomicrobium vannielii ATCC 17100 ans, aatJ, aatQ, aatM, aatP
Rhodopseudomonas palustris CGA009 aapJ, aapQ, aapM, aapP, ans
Rhodospirillum centenum SW; ATCC 51521 bztA, bztB, bztC, bztD, ans
Rhodospirillum rubrum ATCC 11170 ans, aatJ, aatQ, aatM, aatP
Roseburia faecis M72 yhiT, ans
Saccharomonospora cyanea NA-134 ansP, ans
Sedimenticola selenatireducens DSM 17993 ans, dauA
Shewanella amazonensis SB2B ans, glt
Shewanella loihica PV-4 ans, glt
Shewanella oneidensis MR-1 ans, glt
Shewanella sp. ANA-3 ans, glt
Sinorhizobium fredii NGR234 ans, aapJ, aapQ, aapM, aapP
Sinorhizobium medicae WSM419 ans, aapJ, aapQ, aapM, aapP
Sinorhizobium meliloti 1021 ans, aapJ, aapQ, aapM, aapP
Sphingomonas koreensis DSMZ 15582 ans, glt
Stenotrophomonas chelatiphaga DSM 21508 ans, glt
Steroidobacter denitrificans DSM 18526 ans, dauA
Stutzerimonas stutzeri A1501 ans, glt
Sulfuricurvum kujiense DSM 16994 ans, dauA
Sulfurihydrogenibium azorense Az-Fu1 ans, glt
Sulfurihydrogenibium subterraneum DSM 15120 ans, glt
Sulfurimonas denitrificans DSM 1251 ans, glt
Sulfuritalea hydrogenivorans DSM 22779 ans, aatJ, aatQ, aatM, aatP
Sulfurivirga caldicuralii DSM 17737 ans, glt
Synechococcus elongatus PCC 7942 ans, natF, bgtB', natH, bgtA
Teredinibacter turnerae T7901 agcS, ans
Thauera aminoaromatica S2 agcS, ans
Thermithiobacillus tepidarius DSM 3134 ans, glt
Thermocrinis albus DSM 14484 ans, glt
Thermodesulforhabdus norvegica DSM 9990 aapJ, aapQ, aapM, aapP, ans
Thermomonospora curvata DSM 43183 ans, glt
Thermovibrio ammonificans HB-1 ans, glt
Thermus aquaticus YT-1 agcS, ans
Thioalkalivibrio denitrificans ALJD ans, glt
Thioalkalivibrio halophilus HL17 ans, glt
Thioalkalivibrio paradoxus ARh 1 agcS, ans
Thioalkalivibrio thiocyanodenitrificans ARhD 1 ans, glt
Thiohalomonas denitrificans HLD2 agcS, ans
Thiohalospira halophila HL 3 ans, dauA
Thiomicrorhabdus arctica DSM 13458 agcS, ans
Thiomicrorhabdus chilensis DSM 12352 agcS, ans
Thiomicrospira cyclica ALM1 ans, glt
Thiomicrospira microaerophila ASL8-2 ans, dauA
Thiomicrospira pelophila DSM 1534 ans, glt
Thiothrix lacustris DSM 21227 ans, glt
Tistlia consotensis USBA 355 ans, aapJ, aapQ, aapM, aapP
Trichlorobacter lovleyi SZ yhiT, ans
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome ans, natF, bgtB', natH, bgtA
Trichormus variabilis ATCC 29413 ans, natF, natG, natH, bgtA
Xanthobacter autotrophicus Py2 ans, bztA, bztB, bztC, bztD
Xenophilus azovorans DSM 13620 ans, aatJ, aatQ, aatM, aatP

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory