GapMind for Amino acid biosynthesis

 

L-proline biosynthesis

Analysis of pathway pro in 206 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 proB, proA, proC
Acidithiobacillus ferrooxidans ATCC 23270 proB, proA, proC
Acidovorax sp. GW101-3H11 argA, argB, argC, argD, argE, cyclodeaminase
Algiphilus aromaticivorans DG1253 proB, proA, proC
Alicycliphilus denitrificans K601 argJ, argB, argC, argD, cyclodeaminase
Alkalihalobacterium alkalinitrilicum DSM 22532 argJ, argB, argC, argD, OAT, proC
Allochromatium vinosum DSM 180 proB, proA, proC
Ammonifex degensii KC4 proB, proA, proC
Anaerobutyricum hallii DSM 3353 proB, proA, proC
Aquimarina longa SW024 argA, argB, argC, argD, argE?, OAT, proC
Archaeoglobus veneficus SNP6 argJ, argB, argC, argD, cyclodeaminase
Arcobacter nitrofigilis DSM 7299 proB, proA, proC
Azoarcus olearius BH72 argJ, argB, argC, argD, OAT, proC
Azohydromonas australica DSM 1124 argJ, argB, argC, argD, cyclodeaminase
Azorhizobium caulinodans ORS 571 proB, proA, proC
Azospirillum brasilense Sp245 argA, argB, argC, argD, argE, OAT, proC
Azospirillum sp. B510 argA, argB, argC, argD, argE, cyclodeaminase
Bacteroides thetaiotaomicron VPI-5482 proB, proA, proC
Beijerinckia indica subsp. indica ATCC 9039 argA, argB, argC, argD, argE, OAT, proC
Beijerinckia mobilis UQM 1969 argA, argB, argC, argD, argE, OAT, proC
Bradyrhizobium sp. BTAi1 proB, proA, proC
Brevundimonas sp. GW460-12-10-14-LB2 proB, proA, proC
Burkholderia phytofirmans PsJN proB, proA, proC
Burkholderia vietnamiensis G4 proB, proA, proC
Calditerrivibrio nitroreducens DSM 19672 proB, proA, proC
Caminibacter mediatlanticus TB-2 proB, proA, proC
Carboxydothermus pertinax Ug1 proB, proA, proC
Caulobacter crescentus NA1000 proB, proA, proC
Cereibacter sphaeroides ATCC 17029 proB, proA, proC
Chlorobaculum parvum NCIB 8327 proB, proA, proC
Chlorobaculum tepidum TLS proB, proA, proC
Chlorobium limicola DSM 245 proB, proA, proC
Chlorobium phaeobacteroides BS1 proB, proA, proC
Clostridium acetobutylicum ATCC 824 proB, proA, proC
Clostridium kluyveri DSM 555 proB, proA, proC
Clostridium tyrobutyricum FAM22553 argJ, argB, argC, argD, OAT, proC
Crocosphaera subtropica ATCC 51142 argJ, argB, argC, argD, cyclodeaminase
Cupriavidus basilensis FW507-4G11 argA, argB, argC, argD, argE, cyclodeaminase
Dechloromonas agitata is5 argJ, argB, argC, argD, OAT, proC
Dechlorosoma suillum PS proB, proA, proC
Dehalococcoides mccartyi 195 proB, proA, proC
Denitrovibrio acetiphilus DSM 12809 proB, proA, proC
Derxia gummosa DSM 723 proB, proA, proC
Desulfacinum hydrothermale DSM 13146 argJ, argB, argC, argD, OAT, proC
Desulfacinum infernum DSM 9756 argJ, argB, argC, argD, OAT, proC
Desulfarculus baarsii DSM 2075 proB, proA, proC
Desulfatibacillum aliphaticivorans DSM 15576 proB, proA, proC
Desulfatiglans anilini DSM 4660 proB, proA, proC
Desulfitobacterium hafniense DCB-2 proB, proA, proC
Desulfobacca acetoxidans DSM 11109 proB, proA, proC
Desulfobacter vibrioformis DSM 8776 argJ, argB, argC, argD, OAT, proC
Desulfogranum mediterraneum DSM 13871 proB, proA, proC
Desulforamulus ruminis DSM 2154 argJ, argB, argC, argD, OAT, proC
Desulfoscipio geothermicus DSM 3669 proB, proA, proC
Desulfotalea psychrophila LSv54 proB, proA, proC
Desulfovibrio oxyclinae DSM 11498 argJ, argB, argC, argD, OAT, proC
Desulfovibrio vulgaris Hildenborough JW710 proB, proA, proC
Desulfovibrio vulgaris Miyazaki F proB, proA, proC
Desulfurobacterium atlanticum DSM 15668 proB, proA, proC
Desulfuromonas acetexigens DSM 1397 proB, proA, proC
Desulfuromusa kysingii DSM 7343 argJ, argB, argC, argD, OAT, proC
Dinoroseobacter shibae DFL-12 argJ, argB, argC, argD, cyclodeaminase
Dyella japonica UNC79MFTsu3.2 proB, proA, proC
Echinicola vietnamensis KMM 6221, DSM 17526 proB, proA, proC
Escherichia coli BW25113 proB, proA, proC
Ferroglobus placidus DSM 10642 argJ, argB, argC, argD, cyclodeaminase
Frankia alni ACN14a proB, proA, proC
Geobacter metallireducens GS-15 proB, proA, proC
Geotalea uraniireducens Rf4 proB, proA, proC
Halococcus hamelinensis 100A6 lysW, argX, lysZ, lysY, lysJ, lysK, cyclodeaminase
Haloechinothrix alba DSM 45207 argJ, argB, argC, argD, OAT, proC
Haloferax volcanii DS2 lysW, argX, lysZ, lysY, lysJ, lysK, cyclodeaminase
Haloglycomyces albus DSM 45210 argJ, argB, argC, argD, cyclodeaminase
Halomonas desiderata SP1 proB, proA, proC
Halorhodospira halophila SL1 proB, proA, proC
Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547 proB, proA, proC
Herbaspirillum autotrophicum IAM 14942 argA, argB, argC, argD, argE, cyclodeaminase
Herbaspirillum seropedicae SmR1 argA, argB, argC, argD, argE, cyclodeaminase
Hippea alviniae EP5-r proB, proA, proC
Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512 argJ, argB, argC, argD, cyclodeaminase
Hydrogenovibrio halophilus DSM 15072 proB, proA, proC
Hydrogenovibrio kuenenii DSM 12350 proB, proA, proC
Hydrogenovibrio marinus DSM 11271 proB, proA, proC
Hyphomicrobium sulfonivorans WDL6 proB, proA, proC
Klebsiella michiganensis M5al proB, proA, proC
Klebsiella variicola At-22 proB, proA, proC
Kyrpidia tusciae DSM 2912 argJ, argB, argC, argD, OAT, proC
Leptospirillum ferrooxidans C2-3 proB, proA, proC
Lysobacter soli OAE881 proB, proA, proC
Magnetospirillum magneticum AMB-1 proB, proA, proC
Malonomonas rubra DSM 5091 proB, proA, proC
Maridesulfovibrio bastinii DSM 16055 argJ, argB, argC, argD, OAT, proC
Maridesulfovibrio zosterae DSM 11974 argJ, argB, argC, argD, OAT, proC
Marinobacter adhaerens HP15 proB, proA, proC
Mesorhizobium ciceri biovar biserrulae WSM1271 argA, argB, argC, argD, argE, cyclodeaminase
Methanobacterium lacus AL-21 argJ, argB, argC, argD, cyclodeaminase
Methanococcus aeolicus Nankai-3 argJ, argB, argC, argD, cyclodeaminase
Methanococcus maripaludis C5 argJ, argB, argC, argD, cyclodeaminase
Methanosarcina acetivorans C2A proB, proA, proC
Methanosarcina mazei Go1 proB, proA, proC
Methanospirillum lacunae Ki8-1 argJ, argB, argC, argD, cyclodeaminase
Methanothermobacter thermautotrophicus str. Delta H argJ, argB, argC, argD, cyclodeaminase
Methylobacterium nodulans ORS 2060 argA, argB, argC, argD, argE, cyclodeaminase
Methylobacterium sp. 4-46 Apr-46 argA, argB, argC, argD, argE, cyclodeaminase
Methylocapsa acidiphila B2 argA, argB, argC, argD, argE, OAT, proC
Methylocapsa aurea KYG argA, argB, argC, argD, argE, OAT, proC
Methylocella silvestris BL2 argA, argB, argC, argD, argE, OAT, proC
Methylococcus capsulatus str. Bath proB, proA, proC
Methylocystis bryophila S285 argA, argB, argC, argD, argE, OAT, proC
Methyloferula stellata AR4 AR4T proB, proA, proC
Methylohalobius crimeensis 10Ki proB, proA, proC
Methylomonas methanica MC09 proB, proA, proC
Methylosarcina fibrata AML-C10 argJ, argB, argC, argD, cyclodeaminase
Methylotuvimicrobium alcaliphilum 20Z argJ, argB, argC, argD, cyclodeaminase
Methylovulum miyakonense HT12 proB, proA, proC
Mucilaginibacter yixingensis DSM 26809 proB, proA, proC
Mycolicibacterium vanbaalenii PYR-1 argJ, argB, argC, argD, OAT, proC
Nitratifractor salsuginis DSM 16511 proB, proA, proC
Nitratiruptor tergarcus DSM 16512 proB, proA, proC
Nitriliruptor alkaliphilus DSM 45188 argA, argB, argC, argD, argE, OAT, proC
Nitrosopumilus maritimus SCM1 lysW, argX, lysZ, lysY, lysJ, lysK, cyclodeaminase
Nocardioides dokdonensis FR1436 argJ, argB, argC, argD, OAT, proC
Nocardiopsis lucentensis DSM 44048 proB*, proA, proC
Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102 argJ, argB, argC, argD, OAT, proC
Novosphingobium aromaticivorans DSM 12444 proB, proA, proC
Oleispira antarctica RB-8 proB, proA, proC
Paraburkholderia atlantica CCGE1002 proB, proA, proC
Paraburkholderia bryophila 376MFSha3.1 proB, proA, proC
Paraburkholderia phymatum STM815 proB, proA, proC
Paucidesulfovibrio gracilis DSM 16080 argJ, argB, argC, argD, OAT, proC
Pedobacter sp. GW460-11-11-14-LB5 proB, proA, proC
Pelobacter propionicus DSM 2379 proB, proA, proC
Persephonella marina EX-H1 proB, proA, proC
Phaeacidiphilus oryzae TH49 argJ, argB, argC, argD, OAT, proC
Phaeobacter inhibens BS107 argA, argB, argC, argD, argE, cyclodeaminase
Polaromonas naphthalenivorans CJ2 argJ, argB, argC, argD, cyclodeaminase
Prosthecochloris aestuarii DSM 271 proB, proA, proC
Pseudarthrobacter sulfonivorans Ar51 proB, proA, proC
Pseudomonas benzenivorans DSM 8628 proB, proA, proC
Pseudomonas fluorescens FW300-N1B4 argA, argB, argC, argD, argE, cyclodeaminase
Pseudomonas fluorescens FW300-N2C3 argA, argB, argC, argD, argE, cyclodeaminase
Pseudomonas fluorescens FW300-N2E2 proB, proA, proC
Pseudomonas fluorescens FW300-N2E3 argA, argB, argC, argD, argE, cyclodeaminase
Pseudomonas fluorescens GW456-L13 proB, proA, proC
Pseudomonas putida KT2440 argA, argB, argC, argD, argE, cyclodeaminase
Pseudomonas simiae WCS417 argA, argB, argC, argD, argE, cyclodeaminase
Pseudomonas stutzeri RCH2 proB, proA, proC
Pyrolobus fumarii 1A lysW, argX, lysZ, lysY, lysJ, lysK, cyclodeaminase?
Rhizobium etli CFN 42 argA, argB, argC, argD, argE, OAT, proC
Rhizobium johnstonii 3841 argA, argB, argC, argD, argE, OAT, proC
Rhizobium leguminosarum bv. trifolii WSM1325 argA, argB, argC, argD, argE, OAT, proC
Rhizorhabdus wittichii RW1 argA, argB, argC, argD, argE, cyclodeaminase
Rhodanobacter denitrificans FW104-10B01 argA, argB, argC, argD, argE, OAT, proC
Rhodomicrobium vannielii ATCC 17100 argJ, argB, argC, argD, OAT, proC
Rhodopseudomonas palustris CGA009 proB, proA, proC
Rhodospirillum centenum SW SW; ATCC 51521 argJ, argB, argC, argD, OAT, proC
Rhodospirillum rubrum ATCC 11170 argJ, argB, argC, argD, OAT, proC
Roseburia faecis M72 proB, proA, proC
Saccharomonospora cyanea NA-134 argJ, argB, argC, argD, OAT, proC
Sedimenticola selenatireducens DSM 17993 argA, argB, argC, argD, argE, cyclodeaminase
Shewanella amazonensis SB2B proB, proA, proC
Shewanella loihica PV-4 proB, proA, proC
Shewanella oneidensis MR-1 proB, proA, proC
Shewanella sp. ANA-3 proB, proA, proC
Sinorhizobium fredii NGR234 argA, argB, argC, argD, argE, OAT, proC
Sinorhizobium medicae WSM419 argA, argB, argC, argD, argE, cyclodeaminase
Sinorhizobium meliloti 1021 argA, argB, argC, argD, argE, cyclodeaminase
Sphingomonas koreensis DSMZ 15582 proB, proA, proC
Stenotrophomonas chelatiphaga DSM 21508 proB, proA, proC
Steroidobacter denitrificans DSM 18526 proB, proA, proC
Stutzerimonas stutzeri A1501 proB, proA, proC
Sulfuricurvum kujiense DSM 16994 proB, proA, proC
Sulfurihydrogenibium azorense Az-Fu1 proB, proA, proC
Sulfurihydrogenibium subterraneum DSM 15120 proB, proA, proC
Sulfurimonas denitrificans DSM 1251 proB, proA, proC
Sulfuritalea hydrogenivorans sk43H DSM 22779 proB, proA, proC
Sulfurivirga caldicuralii DSM 17737 proB, proA, proC
Synechococcus elongatus PCC 7942 proB, proA, proC
Teredinibacter turnerae T7901 proB, proA, proC
Thauera aminoaromatica S2 argJ, argB, argC, argD, cyclodeaminase
Thermithiobacillus tepidarius DSM 3134 proB, proA, proC
Thermoanaerobacter kivui LKT-1 proB, proA, proC
Thermocrinis albus DSM 14484 proB, proA, proC
Thermodesulforhabdus norvegica DSM 9990 proB, proA, proC
Thermomonospora curvata DSM 43183 argJ, argB, argC, argD, OAT, proC
Thermovibrio ammonificans HB-1 proB, proA, proC
Thermus aquaticus YT-1 proB, proA, proC
Thioalkalivibrio denitrificans ALJD proB, proA, proC
Thioalkalivibrio halophilus HL17 proB, proA, proC
Thioalkalivibrio paradoxus ARh 1 proB, proA, proC
Thioalkalivibrio thiocyanodenitrificans ARhD 1 proB, proA, proC
Thiohalomonas denitrificans HLD2 proB, proA, proC
Thiohalospira halophila DSM 15071 HL 3 proB, proA, proC
Thiomicrorhabdus arctica DSM 13458 proB, proA, proC
Thiomicrorhabdus chilensis DSM 12352 proB, proA, proC
Thiomicrospira cyclica ALM1 proB, proA, proC
Thiomicrospira microaerophila ASL8-2 proB, proA, proC
Thiomicrospira pelophila DSM 1534 proB, proA, proC
Thiothrix lacustris DSM 21227 proB, proA, proC
Tistlia consotensis USBA 355 proB, proA, proC
Trichlorobacter lovleyi SZ proB, proA, proC
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome argJ, argB, argC, argD, cyclodeaminase
Trichormus variabilis ATCC 29413 argJ, argB, argC, argD, OAT, proC
Xanthobacter autotrophicus Py2 proB, proA, proC
Xanthomonas campestris pv. campestris strain 8004 proB, proA, proC
Xenophilus azovorans DSM 13620 argA, argB, argC, argD, argE, cyclodeaminase

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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