L-asparagine catabolism

GapMind for catabolism of small carbon sources

L-asparagine catabolism

Analysis of pathway asparagine in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	ans, BPHYT_RS17540
Acidithiobacillus ferrooxidans ATCC 23270	ans, BPHYT_RS17540
Alicycliphilus denitrificans K601	ans, aatJ, aatQ, aatM, aatP
Allochromatium vinosum DSM 180	ans, glt
Ammonifex degensii KC4	ans, glt
Archaeoglobus veneficus SNP6	ans, glt
Arcobacter nitrofigilis DSM 7299	ans, glt
Azoarcus sp. 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 lipoferum B510	ans, glt
Bacillus alkalinitrilicus DSM 22532	ans, glt
Beijerinckia indica ATCC 9039	ans, aapJ, aapQ, aapM, aapP
Beijerinckia mobilis UQM 1969	ans, aapJ, aapQ, aapM, aapP
Bradyrhizobium sp. BTAi1	aapJ, aapQ, aapM, aapP, ans
Burkholderia vietnamiensis G4	ans, aatJ, aatQ, aatM, aatP
Calditerrivibrio nitroreducens DSM 19672	ans, dauA
Caminibacter mediatlanticus TB-2	ans, glt
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	ansP, ans
Crocosphaera subtropica ATCC 51142	ans, natF, bgtB', natH, bgtA
Dechloromonas agitata is5	ans, glt
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
Desulfallas geothermicus DSM 3669	glnQ, glnP, ans
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
Desulfobulbus mediterraneus DSM 13871	ans, dauA
Desulfotalea psychrophila LSv54	ans, glt
Desulfotomaculum ruminis DSM 2154	ans, glt
Desulfovibrio bastinii DSM 16055	ans, aapJ, aapQ, aapM, aapP
Desulfovibrio gracilis DSM 16080	ans, glt
Desulfovibrio oxyclinae DSM 11498	ans, glt
Desulfovibrio zosterae DSM 11974	ans, aapJ, aapQ, aapM, aapP
Desulfurobacterium atlanticum DSM 15668	ans, glt
Desulfuromonas acetexigens	yhiT, ans
Desulfuromusa kysingii DSM 7343	yhiT, ans
Ferroglobus placidus DSM 10642	ans, glt
Frankia alni ACN14A	ans, glt
Geobacter lovleyi SZ	yhiT, ans
Geobacter metallireducens GS-15	ans, glt
Geobacter uraniireducens Rf4	ans, glt
Haloechinothrix alba DSM 45207	agcS, ans
Haloglycomyces albus DSM 45210	ans, glt
Halomonas desiderata SP1	ans, dauA
Halorhodospira halophila SL1	agcS, ans
Heliobacterium modesticaldum Ice1; ATCC 51547	agcS, ans
Herbaspirillum autotrophicum IAM 14942	ans, aatJ, aatQ, aatM, aatP
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 variicola At-22	ans, aatJ, aatQ, aatM, aatP
Kyrpidia tusciae DSM 2912	ansP, ans
Leptospirillum ferrooxidans C2-3	ans, glt
Malonomonas rubra DSM 5091	ans, aapJ, aapQ, aapM, aapP
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 barkeri Fusaro	agcS, ans
Methanosarcina mazei Go1	ans, glt
Methanothermobacter thermautotrophicus Delta H	ans, glt
Methylobacterium nodulans ORS 2060	ans, aatJ, aatQ, aatM, aatP
Methylobacterium sp. 4-46	ans, aatJ, aatQ, aatM, aatP
Methylocapsa acidiphila B2	ans, aapJ, aapQ, aapM, aapP
Methylocapsa aurea KYG T	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
Methylomicrobium alcaliphilum 20Z	ans, glt
Methylomonas methanica MC09	agcS, ans
Methylosarcina fibrata AML-C10	agcS, ans
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
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 phymatum STM815	ans, aatJ, aatQ, aatM, aatP
Paraburkholderia sp. CCGE1002	ans, aatJ, aatQ, aatM, aatP
Pelobacter propionicus DSM 2379	ans, SLC7A13
Persephonella marina EX-H1	ans, glt
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 stutzeri A1501	ans, glt
Pyrolobus fumarii 1A	ans, glt
Rhizobium etli CFN 42	ans, aapJ, aapQ, aapM, aapP
Rhizobium leguminosarum 3841	ans, aapJ, aapQ, aapM, aapP
Rhizobium leguminosarum WSM1325	ans, aapJ, aapQ, aapM, aapP
Rhodobacter sphaeroides ATCC 17029	ans, bztA, bztB, bztC, bztD
Rhodomicrobium vannielii ATCC 17100	ans, aatJ, aatQ, aatM, aatP
Rhodopseudomonas palustris CGA009	ans, aapJ, aapQ, aapM, aapP
Rhodospirillum centenum SW; ATCC 51521	ans, bztA, bztB, bztC, bztD
Rhodospirillum rubrum ATCC 11170	ans, aatJ, aatQ, aatM, aatP
Saccharomonospora cyanea NA-134	ansP, ans
Sedimenticola selenatireducens DSM 17993	ans, dauA
Sinorhizobium fredii NGR234	ans, aapJ, aapQ, aapM, aapP
Sinorhizobium medicae WSM419	ans, aapJ, aapQ, aapM, aapP
Sphingomonas wittichii RW1	ans, glt
Stenotrophomonas chelatiphaga DSM 21508	ans, glt
Steroidobacter denitrificans DSM 18526	ans, dauA
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
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	ans, aapJ, aapQ, aapM, aapP
Thermomonospora curvata DSM 43183	ans, glt
Thermovibrio ammonificans HB-1	ans, glt
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
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
Trichodesmium erythraeum IMS101	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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources