GapMind for catabolism of small carbon sources

 

L-asparagine catabolism

Analysis of pathway asparagine in 276 genomes

Genome Best path
Acidovorax caeni R-24608 ans, aatJ, aatQ, aatM, aatP
Actinokineospora bangkokensis 44EHW ansP, ans
Actinomyces timonensis 7400942 ansP, ans
Algiphilus aromaticivorans DG1253 ans, dauA
Algoriphagus aquaeductus T4 ans, glt
Algoriphagus machipongonensis PR1 ans, glt
Alicyclobacillus ferrooxydans TC-34 ans, glt
Alishewanella agri BL06 ans, glt
Alistipes indistinctus YIT 12060 yhiT, ans
Alistipes shahii WAL 8301 ans, glt
Alkalitalea saponilacus SC/BZ-SP2 ans, glt
Amantichitinum ursilacus IGB-41 ans, aatJ, aatQ, aatM, aatP
Amphibacillus jilinensis Y1 ans, natF, natG, natH, bgtA
Amphritea japonica JAMM 1866 agcS, ans
Amycolatopsis halophila YIM 93223 agcS, ans
Amycolatopsis xylanica CPCC 202699 ansP, ans
Aquimarina agarilytica ZC1 ans, glt
Aquimarina longa SW024 ans, glt
Aquimarina macrocephali JAMB N27 ans, glt
Archaeoglobus sulfaticallidus PM70-1 ans, glt
Arcticibacter svalbardensis MN12-7 ans, glt
Ardenticatena maritima 110S ans, natF, bgtB', natH, bgtA
Arenimonas metalli CF5-1 ans, glt
Arenitalea lutea P7-3-5 ans, glt
Azospirillum humicireducens SgZ-5 ans, glt
Azospirillum thiophilum BV-S ans, glt
Bacillus altitudinis 41KF2b ans, glt
Bacillus coahuilensis m4-4 agcS, ans
Bacillus cytotoxicus NVH 391-98 ans, glt
Bacillus horneckiae 1P01SC ans, glt
Bacillus okhensis Kh10-101 ans, glt
Bacillus safensis FO-36b ans, glt
Bacillus velezensis CBMB205 ans, glt
Bacteroides clarus YIT 12056 yhiT, ans
Bacteroides faecis MAJ27 yhiT, ans
Bacteroides fluxus YIT 12057 yhiT, ans
Bacteroides oleiciplenus YIT 12058 ans, glt
Barnesiella intestinihominis YIT 11860 ans, dauA
Belnapia rosea CPCC 100156 ans, glt
Bizionia argentinensis JUB59 ans, glt
Bradyrhizobium diazoefficiens USDA110 ans, aatJ, aatQ, aatM, aatP
Brevibacterium jeotgali SJ5-8 ans, dauA
Brucella inopinata BO1 ans, aapJ, aapQ, aapM, aapP
Brucella microti CCM 4915 ans, aapJ, aapQ, aapM, aapP
Bryobacter aggregatus MPL3 ans, glt
Caldicellulosiruptor hydrothermalis 108 ans, glt
Caldicellulosiruptor kronotskyensis 2002 ans, glt
Carboxydothermus pertinax Ug1 ans, glt
Catellicoccus marimammalium M35/04/3 ans, acaP
Chromobacterium vaccinii MWU205 ans, aatJ, aatQ, aatM, aatP
Chryseobacterium angstadtii KM ans, glt
Chryseobacterium arthrosphaerae CC-VM-7 ans, glt
Chryseobacterium viscerum 687B-08 ans, glt
Cloacibacillus porcorum CL-84 ans, glt
Cobetia crustatorum JO1 ans, glt
Collimonas arenae Ter10 ans, aatJ, aatQ, aatM, aatP
Collimonas pratensis Ter91 ans, aatJ, aatQ, aatM, aatP
Collinsella tanakaei YIT 12063 ans, peb1A, peb1B, peb1C, peb1D
Coprobacter fastidiosus NSB1 ans, dauA
Corynebacterium deserti GIMN1.010 ans, glt
Corynebacterium frankenforstense ST18 ansP, ans
Corynebacterium lactis RW2-5 ansP, ans
Croceitalea dokdonensis DOKDO 023 ans, glt
Cronobacter condimenti 1330 ans, aatJ, aatQ, aatM, aatP
Cronobacter muytjensii ATCC 51329 ans, aatJ, aatQ, aatM, aatP
Cronobacter universalis NCTC 9529 ans, aatJ, aatQ, aatM, aatP
Desulfatitalea tepidiphila S28bF ans, natF, bgtB', natH, bgtA
Desulfotomaculum hydrothermale Lam5 ans, glt
Dethiosulfovibrio salsuginis USBA 82 ans, glt
Devosia chinhatensis IPL18 ans, aapJ, aapQ, aapM, aapP
Devriesea agamarum IMP2 ansP, ans
Dialister succinatiphilus YIT 11850 ans, glt
Dietzia timorensis ID05-A0528 ans, glt
Dokdonella koreensis DS-123 ans, dauA
Domibacillus robiginosus WS 4628 ans, glt
Duganella sacchari Sac-22 ans, glt
Dyadobacter tibetensis Y620-1 ans, glt
Dyella jiangningensis SBZ3-12 ans, BPHYT_RS17540
Endozoicomonas montiporae CL-33 ans, glt
Enterococcus termitis LMG 8895 glnQ, glnP, ans
Enterorhabdus caecimuris B7 ans, glt
Epibacterium ulvae U95 ans, bztA, bztB, bztC, bztD
Erythrobacter gangjinensis K7-2 agcS, ans
Erythrobacter marinus HWDM-33 agcS, ans
Ethanoligenens harbinense YUAN-3 agcS, ans
Fervidicella metallireducens AeB ans, glt
Fibrella aestuarina BUZ 2 ans, glt
Flammeovirga pacifica WPAGA1 ans, glt
Flaviramulus ichthyoenteri Th78 ans, glt
Flavobacterium beibuense F44-8 ans, glt
Flavobacterium glycines Gm-149 ans, glt
Flavobacterium sp. LM5 ans, glt
Flavobacterium ummariense DS-12 ans, glt
Frischella perrara PEB0191 ans, aatJ, aatQ, aatM, aatP
Galbibacter marinus ck-I2-15 ans, glt
Gallaecimonas xiamenensis 3-C-1 ans, glt
Geobacter daltonii FRC-32 yhiT, ans
Gillisia marina CBA3202 ans, glt
Gracilibacillus halophilus YIM-C55.5 ans, glt
Granulicella mallensis MP5ACTX8 ans, glt
Granulicella tundricola MP5ACTX9 ans, glt
Hafnia paralvei ATCC 29927 ans, aatJ, aatQ, aatM, aatP
Haladaptatus cibarius D43 ans, glt
Halioglobus japonicus S1-36 ans, glt
Halobacillus alkaliphilus FP5 ans, glt
Halococcus hamelinensis 100A6 ans, glt
Halomonas salina B6 ans, glt
Halomonas smyrnensis AAD6 ans, glt
Halomonas stevensii S18214 ans, dauA
Halomonas titanicae BH1 ans, glt
Halomonas xinjiangensis TRM 0175 agcS, ans
Halopiger salifodinae KCY07-B2 ans, glt
Halostagnicola larsenii XH-48 ans, glt
Haloterrigena daqingensis JX313 ans, glt
Herbaspirillum aquaticum IEH 4430 ans, aatJ, aatQ, aatM, aatP
Hippea alviniae EP5-r ans, glt
Hippea jasoniae Mar08-272r ans, glt
Hoeflea phototrophica DFL-43 ans, aapJ, aapQ, aapM, aapP
Hyphomicrobium nitrativorans NL23 ans, dauA
Imtechella halotolerans K1 ans, glt
Indibacter alkaliphilus LW1 ans, glt
Jannaschia aquimarina GSW-M26 ans, bztA, bztB, bztC, bztD
Jeotgalibacillus soli P9 ans, glt
Kangiella geojedonensis YCS-5 ans, glt
Knoellia flava TL1 ans, glt
Kocuria flava HO-9041 ans, glt
Kocuria turfanensis HO-9042 ans, glt
Laceyella sediminis RHA1 ans, glt
Lacinutrix algicola AKS293 ans, glt
Lacinutrix himadriensis E4-9a ans, glt
Lacinutrix mariniflava AKS432 ans, glt
Lactobacillus curieae CCTCC M 2011381 glnQ, glnP, ans
Lactobacillus delbrueckii ZN7a-9 ans, acaP
Lactobacillus hokkaidonensis LOOC260 ans, glt
Lactobacillus oryzae SG293 ans, glt
Lactobacillus pobuzihii E100301 ans, acaP
Lactobacillus shenzhenensis LY-73 ans, acaP
Lactobacillus silagei IWT126 ans, glt
Leeuwenhoekiella blandensis MED217 agcS, ans
Lentibacillus jeotgali Grbi ans, glt
Limnohabitans curvus MWH-C5 ans, aatJ, aatQ, aatM, aatP
Limnohabitans parvus II-B4 ans, aapJ, aapQ, aapM, aapP
Listeria fleischmannii LU2006-1 glnQ, glnP, ans
Luteimonas huabeiensis HB2 ans, yveA
Luteipulveratus mongoliensis MN07-A0370 ansP, ans
Lutibaculum baratangense AMV1 ans, aapJ, aapQ, aapM, aapP
Lysobacter daejeonensis GH1-9 ans, glt
Magnetovibrio blakemorei MV-1 ans, dauA
Marinicella litoralis KMM 3900 ans, glt
Mariniradius saccharolyticus AK6 ans, glt
Marinobacter algicola DG893 ans, glt
Marinobacter guineae M3B ans, glt
Marinobacter psychrophilus 20041 ans, glt
Marinomonas arctica 328 ans, glt
Marivita geojedonensis DPG-138 ans, bztA, bztB, bztC, bztD
Martelella endophytica YC6887 ans, aapJ, aapQ, aapM, aapP
Megamonas funiformis YIT 11815 ans, glt
Mesorhizobium ciceri WSM1271 ans, aapJ, aapQ, aapM, aapP
Methanobacterium arcticum M2 ans, glt
Methanobacterium veterum MK4 ans, glt
Methanocella arvoryzae MRE50 agcS, ans
Methanococcus aeolicus Nankai-3 ans, glt
Methanoculleus horonobensis T10 ans, glt
Methanolinea tarda NOBI-1 ans, glt
Methanosarcina soligelidi SMA-21 ans, glt
Methanospirillum lacunae Ki8-1 ans, glt
Methanospirillum stamsii Pt1 ans, glt
Methylibium petroleiphilum PM1 ans, aatJ, aatQ, aatM, aatP
Methylobacterium gossipiicola Gh-105 ans, aatJ, aatQ, aatM, aatP
Methylocapsa aurea KYG ans, aapJ, aapQ, aapM, aapP
Methylotenera versatilis 301 ans, dauA
Microbacterium profundi Shh49 ans, glt
Microvirga lotononidis WSM3557 ans, aapJ, aapQ, aapM, aapP
Moritella dasanensis ArB 0140 ans, glt
Mucilaginibacter gossypii Gh-67 ans, glt
Mucilaginibacter gossypiicola Gh-48 ans, glt
Mucilaginibacter mallensis MP1X4 ans, glt
Nafulsella turpanensis ZLM-10 ans, glt
Natronomonas moolapensis 8.8.11 ans, glt
Nautilia profundicola AmH ans, glt
Neiella marina J221 ans, glt
Neptunomonas antarctica S3-22 ans, dauA
Nocardioides daejeonensis MJ31 ans, glt
Nocardioides dokdonensis FR1436 ans, glt
Nocardiopsis baichengensis YIM 90130 ans, glt
Nocardiopsis gilva YIM 90087 ans, glt
Novosphingobium barchaimii LL02 ans, glt
Novosphingobium fuchskuhlense FNE08-7 ans, glt
Novosphingobium lindaniclasticum LE124 ans, glt
Oceanisphaera arctica V1-41 ans, glt
Ochrobactrum rhizosphaerae PR17 ans, aapJ, aapQ, aapM, aapP
Ochrobactrum thiophenivorans DSM 7216 ans, aapJ, aapQ, aapM, aapP
Oscillibacter ruminantium GH1 agcS, ans
Paenisporosarcina indica PN2 ans, glt
Palaeococcus pacificus DY20341 ans, glt
Paludibacter propionicigenes WB4 ans, dauA
Pandoraea thiooxydans ATSB16 ans, glt
Pantoea rwandensis LMG 26275 ans, aatJ, aatQ, aatM, aatP
Pedobacter arcticus A12 ans, glt
Photobacterium gaetbulicola Gung47 ans, glt
Photobacterium jeanii R-40508 ans, glt
Phyllobacterium brassicacearum STM 196 ans, aapJ, aapQ, aapM, aapP
Phyllobacterium endophyticum PEPV15 ans, aapJ, aapQ, aapM, aapP
Phyllobacterium leguminum ORS 1419 ans, aapJ, aapQ, aapM, aapP
Planktomarina temperata RCA23 ans, bztA, bztB, bztC, bztD
Planococcus halocryophilus Or1 ans, glt
Pleomorphomonas diazotrophica R5-392 ans, aapJ, aapQ, aapM, aapP
Polaribacter dokdonensis DSW-5 ans, glt
Pontibacillus litoralis JSM 072002 ans, glt
Pontibacter lucknowensis DM9 ans, glt
Pontibacter ramchanderi LP43 ans, glt
Pontimonas salivibrio CL-TW6 ans, natF, natG, natH, bgtA
Porphyrobacter dokdonensis DSW-74 agcS, ans
Pseudoalteromonas arctica A 37-1-2 ans, glt
Pseudomonas baetica a390 ans, aatJ, aatQ, aatM, aatP
Pseudomonas litoralis 2SM5 ans, dauA
Pseudomonas taeanensis MS-3 ans, glt
Pseudovibrio axinellae Ad2 ans, aapJ, aapQ, aapM, aapP
Psychrobacter arcticus 273-4 ans, aatJ, aatQ, aatM, aatP
Psychrobacter cryohalolentis K5 ans, aatJ, aatQ, aatM, aatP
Psychromonas ingrahamii 37 ans, glt
Psychromonas ossibalaenae JAMM 0738 ans, glt
Rhizobium freirei PRF 81 ans, aapJ, aapQ, aapM, aapP
Rhizobium grahamii CCGE 502 ans, aapJ, aapQ, aapM, aapP
Rhizobium subbaraonis JC85 ans, aapJ, aapQ, aapM, aapP
Rhodanobacter denitrificans 2APBS1 ans, glt
Rhodobacter johrii JA192 ans, bztA, bztB, bztC, bztD
Rhodobacter maris JA276 ans, bztA, bztB, bztC, bztD
Rhodobacter ovatus JA234 ans, bztA, bztB, bztC, bztD
Rhodobacter viridis JA737 ans, bztA, bztB, bztC, bztD
Rhodococcus qingshengii djl-6-2 ansP, ans
Rhodopseudomonas pseudopalustris DSM 123 ans, glt
Roseateles aquatilis CCUG 48205 ans, aatJ, aatQ, aatM, aatP
Roseivirga spongicola UST030701-084 ans, glt
Rubrivirga marina SAORIC-28 ans, glt
Ruegeria conchae TW15 ans, bztA, bztB, bztC, bztD
Saccharomonospora marina XMU15 ans, glt
Salinicoccus carnicancri Crm ans, glt
Serinicoccus profundi MCCC 1A05965 ans, glt
Shewanella halifaxensis HAW-EB4 ans, glt
Skermanella stibiiresistens SB22 ans, aapJ, aapQ, aapM, aapP
Snodgrassella alvi wkB2 ans, glt
Sphaerochaeta globosa Buddy ans, peb1A, peb1B, peb1C, peb1D
Sphaerochaeta pleomorpha Grapes ans, glt
Sphingobium baderi LL03 ans, glt
Sphingobium czechense LL01 ans, glt
Sphingobium quisquiliarum P25 ans, glt
Sphingomonas histidinilytica UM2 ans, glt
Sphingomonas indica Dd16 ans, glt
Sphingomonas laterariae LNB2 ans, glt
Sphingopyxis indica DS15 ans, glt
Sphingopyxis terrae UI2 ans, glt
Sporolactobacillus vineae SL153 ans, BPHYT_RS17540
Streptacidiphilus oryzae TH49 ans, BPHYT_RS17540
Streptococcus anginosus CCUG 39159 glnQ, glnP, ans
Streptococcus massiliensis 4401825 glnQ, glnP, ans
Streptococcus oralis 7747 agcS, ans
Streptococcus oralis AZ_3a glnQ, glnP, ans
Streptomyces kebangsaanensis SUK12 ans, glt
Succinatimonas hippei YIT 12066 ans, dauA
Sulfurimonas gotlandica GD1 ans, glt
Tatumella morbirosei LMG 23360 ans, aatJ, aatQ, aatM, aatP
Thauera humireducens SgZ-1 ans, dauA
Thermoactinomyces daqus H-18 ans, glt
Thermobifida halotolerans YIM 90462 ans, dauA
Thermodesulfovibrio aggregans TGE-P1 ans, glt
Thermophagus xiamenensis HS1 ans, glt
Thermovenabulum gondwanense R270 ans, glt
Thioclava dalianensis DLFJ1-1 ans, bztA, bztB, bztC, bztD
Thiohalospira halophila HL 3 ans, dauA
Tistlia consotensis USBA 355 ans, aapJ, aapQ, aapM, aapP
Vagococcus penaei CD276 ans, acaP
Verminephrobacter eiseniae EF01-2 ans, aatJ, aatQ, aatM, aatP
Weissella oryzae SG25 ansP, ans
Williamsia sterculiae CPCC 203464 ansP, ans
Yersinia intermedia Y228 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.

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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