GapMind for catabolism of small carbon sources

 

lactose catabolism

Analysis of pathway lactose in 150 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 lacP, lacZ, galK, galT, galE, pgmA, glk
Acidithiobacillus ferrooxidans ATCC 23270 lacP, lacZ, galK, galT, galE, pgmA, glk
Alicycliphilus denitrificans K601 lacP, lacZ, galK, galT, galE, pgmA, glk
Allochromatium vinosum DSM 180 lacP, lacZ, galK, galT, galE, pgmA, glk
Ammonifex degensii KC4 lacP, lacZ, galK, galT, galE, pgmA, glk
Archaeoglobus veneficus SNP6 lacP, lacZ, galK, galT, galE, pgmA, glk
Arcobacter nitrofigilis DSM 7299 lacP, lacZ, galK, galT, galE, pgmA, glk
Azoarcus sp. BH72 lacP, lacZ, galK, galT, galE, pgmA, glk
Azohydromonas australica DSM 1124 lacP, lacZ, galK, galT, galE, pgmA, glk
Azorhizobium caulinodans ORS 571 lacA', lacC', lacB', klh, MFS-glucose, glk
Azospirillum lipoferum B510 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Bacillus alkalinitrilicus DSM 22532 lacP, lacZ, galK, galT, galE, pgmA, glk
Beijerinckia indica ATCC 9039 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Beijerinckia mobilis UQM 1969 lacA', lacC', lacB', klh, MFS-glucose, glk
Bradyrhizobium sp. BTAi1 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Burkholderia vietnamiensis G4 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Calditerrivibrio nitroreducens DSM 19672 lacP, lacZ, galK, galT, galE, pgmA, glk
Caminibacter mediatlanticus TB-2 lacA', lacC', lacB', klh, ptsG-crr
Chlorobaculum parvum NCIB 8327 lacP, lacZ, galK, galT, galE, pgmA, glk
Chlorobaculum tepidum TLS lacP, lacZ, galK, galT, galE, pgmA, glk
Chlorobium limicola DSM 245 lacP, lacZ, galK, galT, galE, pgmA, glk
Chlorobium phaeobacteroides BS1 lacP, lacZ, galK, galT, galE, pgmA, glk
Clostridium acetobutylicum ATCC 824 lacY, lacZ, galK, galT, galE, pgmA, glk
Clostridium kluyveri DSM 555 lacP, lacZ, galK, galT, galE, pgmA, glk
Crocosphaera subtropica ATCC 51142 lacP, lacZ, galK, galT, galE, pgmA, glk
Dechloromonas agitata is5 lacP, lacZ, galK, galT, galE, pgmA, glk
Dehalococcoides mccartyi 195 lacP, lacZ, galK, galT, galE, pgmA, glk
Denitrovibrio acetiphilus DSM 12809 lacP, lacZ, galK, galT, galE, pgmA, glk
Derxia gummosa DSM 723 lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, glk
Desulfacinum hydrothermale DSM 13146 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfacinum infernum DSM 9756 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfallas geothermicus DSM 3669 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfarculus baarsii DSM 2075 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfatibacillum aliphaticivorans DSM 15576 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfatiglans anilini DSM 4660 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfitobacterium hafniense DCB-2 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfobacca acetoxidans DSM 11109 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfobacter vibrioformis DSM 8776 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfobulbus mediterraneus DSM 13871 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfotalea psychrophila LSv54 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfotomaculum ruminis DSM 2154 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfovibrio bastinii DSM 16055 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfovibrio gracilis DSM 16080 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfovibrio oxyclinae DSM 11498 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfovibrio zosterae DSM 11974 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfurobacterium atlanticum DSM 15668 lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfuromonas acetexigens lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfuromusa kysingii DSM 7343 lacP, lacZ, galK, galT, galE, pgmA, glk
Ferroglobus placidus DSM 10642 lacP, lacZ, galK, galT, galE, pgmA, glk
Frankia alni ACN14A lacP, lacZ, galK, galT, galE, pgmA, glk
Geobacter lovleyi SZ lacP, lacZ, galK, galT, galE, pgmA, glk
Geobacter metallireducens GS-15 lacP, lacZ, galK, galT, galE, pgmA, glk
Geobacter uraniireducens Rf4 lacP, lacZ, galK, galT, galE, pgmA, glk
Haloechinothrix alba DSM 45207 lacP, lacZ, galK, galT, galE, pgmA, glk
Haloglycomyces albus DSM 45210 lacP, lacZ, galK, galT, galE, pgmA, glk
Halomonas desiderata SP1 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Halorhodospira halophila SL1 lacP, lacZ, galK, galT, galE, pgmA, glk
Heliobacterium modesticaldum Ice1; ATCC 51547 lacP, lacZ, galK, galT, galE, pgmA, glk
Herbaspirillum autotrophicum IAM 14942 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Hydrogenophaga taeniospiralis NBRC 102512 lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Hydrogenovibrio halophilus DSM 15072 lacP, lacZ, galK, galT, galE, pgmA, glk
Hydrogenovibrio kuenenii DSM 12350 lacP, lacZ, galK, galT, galE, pgmA, glk
Hydrogenovibrio marinus DSM 11271 lacP, lacZ, galK, galT, galE, pgmA, glk
Hyphomicrobium sulfonivorans WDL6 lacP, lacZ, galK, galT, galE, pgmA, glk
Klebsiella variicola At-22 lacY, lacZ, galK, galT, galE, pgmA, glk
Kyrpidia tusciae DSM 2912 lacP, lacZ, galK, galT, galE, pgmA, glk
Leptospirillum ferrooxidans C2-3 lacP, lacZ, galK, galT, galE, pgmA, glk
Malonomonas rubra DSM 5091 lacP, lacZ, galK, galT, galE, pgmA, glk
Mesorhizobium ciceri WSM1271 lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Methanobacterium lacus AL-21 lacP, lacZ, galK, galT, galE, pgmA, glk
Methanococcus aeolicus Nankai-3 lacA', lacC', lacB', klh, ptsG-crr
Methanococcus maripaludis C5 lacA', lacC', lacB', klh, ptsG-crr
Methanosarcina acetivorans C2A lacP, lacZ, galK, galT, galE, pgmA, glk
Methanosarcina barkeri Fusaro lacP, lacZ, galK, galT, galE, pgmA, glk
Methanosarcina mazei Go1 lacP, lacZ, galK, galT, galE, pgmA, glk
Methanothermobacter thermautotrophicus Delta H lacP, lacZ, galK, galT, galE, pgmA, glk
Methylobacterium nodulans ORS 2060 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Methylobacterium sp. 4-46 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Methylocapsa acidiphila B2 lacP, lacZ, galK, galT, galE, pgmA, glk
Methylocapsa aurea KYG T lacP, lacZ, galK, galT, galE, pgmA, glk
Methylocella silvestris BL2 lacP, lacZ, galK, galT, galE, pgmA, glk
Methylococcus capsulatus Bath lacP, lacZ, galK, galT, galE, pgmA, glk
Methylocystis bryophila S285 lacP, lacZ, galK, galT, galE, pgmA, glk
Methyloferula stellata AR4T lacP, lacZ, galK, galT, galE, pgmA, glk
Methylohalobius crimeensis 10Ki lacP, lacZ, galK, galT, galE, pgmA, glk
Methylomicrobium alcaliphilum 20Z lacP, lacZ, galK, galT, galE, pgmA, glk
Methylomonas methanica MC09 lacP, lacZ, galK, galT, galE, pgmA, glk
Methylosarcina fibrata AML-C10 lacP, lacZ, galK, galT, galE, pgmA, glk
Methylovulum miyakonense HT12 lacP, lacZ, galK, galT, galE, pgmA, glk
Mycolicibacterium vanbaalenii PYR-1 lacP, lacZ, galK, galT, galE, pgmA, glk
Nitratifractor salsuginis DSM 16511 lacP, lacZ, galK, galT, galE, pgmA, glk
Nitratiruptor tergarcus DSM 16512 lacP, lacZ, galK, galT, galE, pgmA, glk
Nitriliruptor alkaliphilus DSM 45188 lacP, lacZ, galK, galT, galE, pgmA, glk
Nocardiopsis lucentensis DSM 44048 lacP, lacZ, galK, galT, galE, pgmA, glk
Nostoc punctiforme ATCC 29133; PCC 73102 lacP, lacZ, galK, galT, galE, pgmA, glk
Novosphingobium aromaticivorans DSM 12444 lacP, lacZ, galK, galT, galE, pgmA, glk
Oleispira antarctica lacP, lacZ, galK, galT, galE, pgmA, glk
Paraburkholderia phymatum STM815 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Paraburkholderia sp. CCGE1002 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Pelobacter propionicus DSM 2379 lacA', lacC', lacB', klh, SemiSWEET, glk
Persephonella marina EX-H1 lacP, lacZ, galK, galT, galE, pgmA, glk
Polaromonas naphthalenivorans CJ2 lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, glk
Prosthecochloris aestuarii DSM 271 lacP, lacZ, galK, galT, galE, pgmA, glk
Pseudarthrobacter sulfonivorans Ar51 lacP, lacZ, galK, galT, galE, pgmA, glk
Pseudomonas benzenivorans DSM 8628 lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas stutzeri A1501 lacP, lacZ, galK, galT, galE, pgmA, glk
Pyrolobus fumarii 1A lacA', lacC', lacB', klh, ptsG-crr
Rhizobium etli CFN 42 lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Rhizobium leguminosarum 3841 lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Rhizobium leguminosarum WSM1325 lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Rhodobacter sphaeroides ATCC 17029 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Rhodomicrobium vannielii ATCC 17100 lacP, lacZ, galK, galT, galE, pgmA, glk
Rhodopseudomonas palustris CGA009 lacP, lacZ, galK, galT, galE, pgmA, glk
Rhodospirillum centenum SW; ATCC 51521 lacP, lacZ, galK, galT, galE, pgmA, glk
Rhodospirillum rubrum ATCC 11170 lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, glk
Saccharomonospora cyanea NA-134 lacP, lacZ, galK, galT, galE, pgmA, glk
Sedimenticola selenatireducens DSM 17993 lacP, lacZ, galK, galT, galE, pgmA, glk
Sinorhizobium fredii NGR234 lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Sinorhizobium medicae WSM419 lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Sphingomonas wittichii RW1 lacA', lacC', lacB', klh, ptsG-crr
Stenotrophomonas chelatiphaga DSM 21508 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Steroidobacter denitrificans DSM 18526 lacP, lacZ, galK, galT, galE, pgmA, glk
Sulfuricurvum kujiense DSM 16994 lacA', lacC', lacB', klh, ptsG-crr
Sulfurihydrogenibium azorense Az-Fu1 lacP, lacZ, galK, galT, galE, pgmA, glk
Sulfurihydrogenibium subterraneum DSM 15120 lacP, lacZ, galK, galT, galE, pgmA, glk
Sulfurimonas denitrificans DSM 1251 lacA', lacC', lacB', klh, ptsG-crr
Sulfuritalea hydrogenivorans DSM 22779 lacP, lacZ, galK, galT, galE, pgmA, glk
Sulfurivirga caldicuralii DSM 17737 lacP, lacZ, galK, galT, galE, pgmA, glk
Teredinibacter turnerae T7901 lacP, lacZ, galK, galT, galE, pgmA, glk
Thauera aminoaromatica S2 lacP, lacZ, galK, galT, galE, pgmA, glk
Thermithiobacillus tepidarius DSM 3134 lacP, lacZ, galK, galT, galE, pgmA, glk
Thermocrinis albus DSM 14484 lacP, lacZ, galK, galT, galE, pgmA, glk
Thermodesulforhabdus norvegica DSM 9990 lacP, lacZ, galK, galT, galE, pgmA, glk
Thermomonospora curvata DSM 43183 lacP, lacZ, galK, galT, galE, pgmA, glk
Thermovibrio ammonificans HB-1 lacP, lacZ, galK, galT, galE, pgmA, glk
Thioalkalivibrio denitrificans ALJD lacP, lacZ, galK, galT, galE, pgmA, glk
Thioalkalivibrio halophilus HL17 lacP, lacZ, galK, galT, galE, pgmA, glk
Thioalkalivibrio paradoxus ARh 1 lacP, lacZ, galK, galT, galE, pgmA, glk
Thioalkalivibrio thiocyanodenitrificans ARhD 1 lacP, lacZ, galK, galT, galE, pgmA, glk
Thiohalomonas denitrificans HLD2 lacP, lacZ, galK, galT, galE, pgmA, glk
Thiomicrorhabdus arctica DSM 13458 lacP, lacZ, galK, galT, galE, pgmA, glk
Thiomicrorhabdus chilensis DSM 12352 lacP, lacZ, galK, galT, galE, pgmA, glk
Thiomicrospira cyclica ALM1 lacP, lacZ, galK, galT, galE, pgmA, glk
Thiomicrospira microaerophila ASL8-2 lacP, lacZ, galK, galT, galE, pgmA, glk
Thiomicrospira pelophila DSM 1534 lacP, lacZ, galK, galT, galE, pgmA, glk
Thiothrix lacustris DSM 21227 lacP, lacZ, galK, galT, galE, pgmA, glk
Trichodesmium erythraeum IMS101 lacA', lacC', lacB', klh, mglA, mglB, mglC, glk
Trichormus variabilis ATCC 29413 lacA', lacC', lacB', klh, SemiSWEET, glk
Xanthobacter autotrophicus Py2 lacA', lacC', lacB', klh, MFS-glucose, glk
Xenophilus azovorans DSM 13620 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk

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