GapMind for catabolism of small carbon sources

 

L-alanine catabolism

Analysis of pathway alanine in 201 genomes

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

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