GapMind for catabolism of small carbon sources

 

putrescine catabolism

Analysis of pathway putrescine in 201 genomes

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

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