GapMind for catabolism of small carbon sources

 

sucrose catabolism

Analysis of pathway sucrose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 sut, SUS, scrK, galU, pgmA
Acidithiobacillus ferrooxidans ATCC 23270 sut, SUS, scrK, galU, pgmA
Acidovorax sp. GW101-3H11 ams, gtsA, gtsB, gtsC, gtsD, glk
Algiphilus aromaticivorans DG1253 sut, scrP, scrK, pgmA
Alicycliphilus denitrificans K601 sut, SUS, scrK, galU, pgmA
Alkalihalobacterium alkalinitrilicum DSM 22532 ams, fruII-ABC, 1pfk, fba, tpi
Allochromatium vinosum DSM 180 sut, ams, scrK, glk
Ammonifex degensii KC4 ams, MFS-glucose, glk
Anaerobutyricum hallii DSM 3353 ams, fruII-ABC, 1pfk, fba, tpi
Aquimarina longa SW024 ams, fruII-ABC, 1pfk, fba, tpi
Archaeoglobus veneficus SNP6 ams, fruII-ABC, 1pfk, fba, tpi
Arcobacter nitrofigilis DSM 7299 sut, SUS, scrK, galU, pgmA
Azoarcus olearius BH72 ams, MFS-glucose, glk
Azohydromonas australica DSM 1124 ams, gtsA, gtsB, gtsC, gtsD, glk
Azorhizobium caulinodans ORS 571 ams, MFS-glucose, glk
Azospirillum brasilense Sp245 ams, mglA, mglB, mglC, glk
Azospirillum sp. B510 ams, mglA, mglB, mglC, glk
Bacteroides thetaiotaomicron VPI-5482 ams, BT1758, scrK
Beijerinckia indica ATCC 9039 ams, mglA, mglB, mglC, glk
Beijerinckia mobilis UQM 1969 ams, MFS-glucose, glk
Billgrantia desiderata SP1 thuE, thuF, thuG, thuK, ams, scrK, glk
Bradyrhizobium sp. BTAi1 ams, mglA, mglB, mglC, glk
Brevundimonas sp. GW460-12-10-14-LB2 ams, fruP, scrK
Burkholderia phytofirmans PsJN ams, gtsA, gtsB, gtsC, gtsD, glk
Burkholderia vietnamiensis G4 ams, gtsA, gtsB, gtsC, gtsD, glk
Calditerrivibrio nitroreducens DSM 19672 sut, SUS, scrK, galU, pgmA
Caminibacter mediatlanticus TB-2 ams, fruII-ABC, 1pfk, fba, tpi
Carboxydothermus pertinax Ug1 ams, fruII-ABC, 1pfk, fba, tpi
Caulobacter crescentus NA1000 scrT, ams, scrK, glk
Cereibacter sphaeroides ATCC 17029 aglE, aglF, aglG, aglK, ams, scrK, glk
Chlorobaculum parvum NCIB 8327 ams, SemiSWEET, glk
Chlorobaculum tepidum TLS ams, SemiSWEET, glk
Chlorobium limicola DSM 245 ams, SemiSWEET, glk
Chlorobium phaeobacteroides BS1 ams, SemiSWEET, glk
Clostridium acetobutylicum ATCC 824 ams, manX, manY, manZ
Clostridium kluyveri DSM 555 ams, MFS-glucose, glk
Clostridium tyrobutyricum FAM22553 ams, fruII-ABC, 1pfk, fba, tpi
Crocosphaera subtropica ATCC 51142 ams, SemiSWEET, glk
Cupriavidus basilensis FW507-4G11 ams, frcA, frcB, frcC, scrK
Dechloromonas agitata is5 sut, SUS, scrK, galU, pgmA
Dechlorosoma suillum PS sut, SUS, scrK, galU, pgmA
Dehalococcoides mccartyi 195 ams, fruII-ABC, 1pfk, fba, tpi
Denitrovibrio acetiphilus DSM 12809 sut, SUS, scrK, galU, pgmA
Derxia gummosa DSM 723 ams, gtsA, gtsB, gtsC, gtsD, glk
Desulfacinum hydrothermale DSM 13146 ams, fruII-ABC, 1pfk, fba, tpi
Desulfacinum infernum DSM 9756 ams, fruII-ABC, 1pfk, fba, tpi
Desulfarculus baarsii DSM 2075 ams, ptsG-crr
Desulfatibacillum aliphaticivorans DSM 15576 ams, fruII-ABC, 1pfk, fba, tpi
Desulfatiglans anilini DSM 4660 ams, MFS-glucose, glk
Desulfitobacterium hafniense DCB-2 ams, MFS-glucose, glk
Desulfobacca acetoxidans DSM 11109 ams, fruII-ABC, 1pfk, fba, tpi
Desulfobacter vibrioformis DSM 8776 sut, ams, scrK, glk
Desulfogranum mediterraneum DSM 13871 sut, SUS, scrK, galU, pgmA
Desulforamulus ruminis DSM 2154 ams, fruII-ABC, 1pfk, fba, tpi
Desulfoscipio geothermicus DSM 3669 ams, fruII-ABC, 1pfk, fba, tpi
Desulfotalea psychrophila LSv54 ams, MFS-glucose, glk
Desulfovibrio oxyclinae DSM 11498 sut, SUS, scrK, galU, pgmA
Desulfovibrio vulgaris Hildenborough JW710 sut, SUS, scrK, galU, pgmA
Desulfovibrio vulgaris Miyazaki F sut, SUS, scrK, galU, pgmA
Desulfurobacterium atlanticum DSM 15668 ams, fruII-ABC, 1pfk, fba, tpi
Desulfuromonas acetexigens ams, fruII-ABC, 1pfk, fba, tpi
Desulfuromusa kysingii DSM 7343 ams, fruII-ABC, 1pfk, fba, tpi
Dinoroseobacter shibae DFL-12 aglE, aglF, aglG, aglK, ams, scrK, glk
Dyella japonica UNC79MFTsu3.2 ams, MFS-glucose, glk
Echinicola vietnamensis KMM 6221, DSM 17526 ams, glcP, scrK
Escherichia coli BW25113 ams, fruA, fruB, 1pfk, fba, tpi
Ferroglobus placidus DSM 10642 sut, SUS, scrK, galU, pgmA
Frankia alni ACN14a ams, MFS-glucose, glk
Geobacter metallireducens GS-15 ams, MFS-glucose, glk
Geotalea uraniireducens Rf4 ams, MFS-glucose, glk
Halococcus hamelinensis 100A6 ams, fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Haloechinothrix alba DSM 45207 ams, MFS-glucose, glk
Haloferax volcanii DS2 ams, fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Haloglycomyces albus DSM 45210 ams, mglA, mglB, mglC, glk
Halorhodospira halophila SL1 sut, SUS, scrK, galU, pgmA
Heliomicrobium modesticaldum Ice1; ATCC 51547 sut, SUS, scrK, galU, pgmA
Herbaspirillum autotrophicum IAM 14942 ams, fruA, fruI, 1pfk, fba, tpi
Herbaspirillum seropedicae SmR1 ams, mglA, mglB, mglC, glk
Hippea alviniae EP5-r sut, SUS, scrK, galU, pgmA
Hydrogenophaga taeniospiralis NBRC 102512 ams, gtsA, gtsB, gtsC, gtsD, glk
Hydrogenovibrio halophilus DSM 15072 sut, ams, scrK, glk
Hydrogenovibrio kuenenii DSM 12350 sut, ams, scrK, glk
Hydrogenovibrio marinus DSM 11271 sut, ams, scrK, glk
Hyphomicrobium sulfonivorans WDL6 ams, MFS-glucose, glk
Klebsiella michiganensis M5al ams, fruA, fruB, 1pfk, fba, tpi
Klebsiella variicola At-22 ams, fruA, fruB, 1pfk, fba, tpi
Kyrpidia tusciae DSM 2912 sut, SUS, scrK, galU, pgmA
Leptospirillum ferrooxidans C2-3 ams, SemiSWEET, glk
Magnetospirillum magneticum AMB-1 sut, SUS, scrK, galU, pgmA
Malonomonas rubra DSM 5091 ams, fruA, fruI, 1pfk, fba, tpi
Maridesulfovibrio bastinii DSM 16055 sut, SUS, scrK, galU, pgmA
Maridesulfovibrio zosterae DSM 11974 ams, fruA, fruI, 1pfk, fba, tpi
Marinobacter adhaerens HP15 ams, gtsA, gtsB, gtsC, gtsD, glk
Mesorhizobium ciceri WSM1271 aglE, aglF, aglG, aglK, ams, scrK, glk
Methanobacterium lacus AL-21 sut, SUS, scrK, galU, pgmA
Methanococcus aeolicus Nankai-3 ams, fruII-ABC, 1pfk, fba, tpi
Methanococcus maripaludis C5 ams, fruII-ABC, 1pfk, fba, tpi
Methanosarcina acetivorans C2A sut, SUS, scrK, galU, pgmA
Methanosarcina mazei Go1 sut, SUS, scrK, galU, pgmA
Methanospirillum lacunae Ki8-1 ams, SemiSWEET, glk
Methanothermobacter thermautotrophicus Delta H sut, SUS, scrK, galU, pgmA
Methylobacterium nodulans ORS 2060 sut, SUS, scrK, galU, pgmA
Methylobacterium sp. 4-46 Apr-46 sacP, scrB, scrK
Methylocapsa acidiphila B2 sut, SUS, scrK, galU, pgmA
Methylocapsa aurea KYG ams, MFS-glucose, glk
Methylocella silvestris BL2 sut, SUS, scrK, galU, pgmA
Methylococcus capsulatus Bath sut, ams, scrK, glk
Methylocystis bryophila S285 ams, SemiSWEET, glk
Methyloferula stellata AR4T sut, SUS, scrK, galU, pgmA
Methylohalobius crimeensis 10Ki sut, SUS, scrK, galU, pgmA
Methylomonas methanica MC09 ams, MFS-glucose, glk
Methylosarcina fibrata AML-C10 ams, MFS-glucose, glk
Methylotuvimicrobium alcaliphilum 20Z ams, SSS-glucose, glk
Methylovulum miyakonense HT12 sut, SUS, scrK, galU, pgmA
Mycolicibacterium vanbaalenii PYR-1 ams, fruII-ABC, 1pfk, fba, tpi
Nitratifractor salsuginis DSM 16511 sut, SUS, scrK, galU, pgmA
Nitratiruptor tergarcus DSM 16512 sut, SUS, scrK, galU, pgmA
Nitriliruptor alkaliphilus DSM 45188 ams, fruII-ABC*, 1pfk, fba, tpi
Nocardioides dokdonensis FR1436 ams, fruII-ABC, 1pfk, fba, tpi
Nocardiopsis lucentensis DSM 44048 ams, frcA, frcB, frcC, scrK
Nostoc punctiforme ATCC 29133; PCC 73102 ams, MFS-glucose, glk
Novosphingobium aromaticivorans DSM 12444 ams, MFS-glucose, glk
Oleispira antarctica sut, SUS, scrK, galU, pgmA
Paraburkholderia atlantica CCGE1002 ams, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia bryophila 376MFSha3.1 ams, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia phymatum STM815 ams, gtsA, gtsB, gtsC, gtsD, glk
Paucidesulfovibrio gracilis DSM 16080 sut, SUS, scrK, galU, pgmA
Pedobacter sp. GW460-11-11-14-LB5 ams, SSS-glucose, glk
Pelobacter propionicus DSM 2379 ams, SemiSWEET, glk
Persephonella marina EX-H1 ams, ptsG-crr
Phaeacidiphilus oryzae TH49 ams, fruII-ABC, 1pfk, fba, tpi
Phaeobacter inhibens BS107 aglE, aglF, aglG, aglK, ams, scrK, glk
Polaromonas naphthalenivorans CJ2 ams, gtsA, gtsB, gtsC, gtsD, glk
Prosthecochloris aestuarii DSM 271 sut, scrP, scrK, pgmA
Pseudarthrobacter sulfonivorans Ar51 ams, mglA, mglB, mglC, glk
Pseudomonas benzenivorans DSM 8628 ams, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N1B4 thuE, thuF, thuG, thuK, ams, scrK, glk
Pseudomonas fluorescens FW300-N2C3 thuE, thuF, thuG, thuK, ams, scrK, glk
Pseudomonas fluorescens FW300-N2E2 thuE, thuF, thuG, thuK, ams, scrK, glk
Pseudomonas fluorescens FW300-N2E3 thuE, thuF, thuG, thuK, ams, scrK, glk
Pseudomonas fluorescens GW456-L13 ams, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas putida KT2440 ams, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas simiae WCS417 ams, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas stutzeri RCH2 ams, gtsA, gtsB, gtsC, gtsD, glk
Pyrolobus fumarii 1A ams, fruII-ABC, 1pfk, fba, tpi
Rhizobium etli CFN 42 thuE, thuF, thuG, thuK, ams, scrK, glk
Rhizobium johnstonii 3841 thuE, thuF, thuG, thuK, ams, scrK, glk
Rhizobium leguminosarum WSM1325 aglE, aglF, aglG, aglK, ams, scrK, glk
Rhizorhabdus wittichii RW1 sut, SUS, scrK, galU, pgmA
Rhodanobacter denitrificans FW104-10B01 ams, MFS-glucose, glk
Rhodomicrobium vannielii ATCC 17100 sut, SUS, scrK, galU, pgmA
Rhodopseudomonas palustris CGA009 ams, fruII-ABC, 1pfk, fba, tpi
Rhodospirillum centenum SW; ATCC 51521 thuE, thuF, thuG, thuK, ams, scrK, glk
Rhodospirillum rubrum ATCC 11170 ams, gtsA, gtsB, gtsC, gtsD, glk
Roseburia faecis M72 ams, fruII-ABC, 1pfk, fba, tpi
Saccharomonospora cyanea NA-134 ams, MFS-glucose, glk
Sedimenticola selenatireducens DSM 17993 sut, SUS, scrK, galU, pgmA
Shewanella amazonensis SB2B ams, MFS-glucose, glk
Shewanella loihica PV-4 ams, MFS-glucose, glk
Shewanella oneidensis MR-1 ams, ptsG, crr
Shewanella sp. ANA-3 scrT, scrP, scrK, pgmA
Sinorhizobium fredii NGR234 thuE, thuF, thuG, thuK, ams, scrK, glk
Sinorhizobium medicae WSM419 thuE, thuF, thuG, thuK, ams, scrK, glk
Sinorhizobium meliloti 1021 thuE, thuF, thuG, thuK, ams, scrK, glk
Sphingomonas koreensis DSMZ 15582 ams, MFS-glucose, glk
Stenotrophomonas chelatiphaga DSM 21508 ams, MFS-glucose, glk
Steroidobacter denitrificans DSM 18526 ams, MFS-glucose, glk
Stutzerimonas stutzeri A1501 ams, gtsA, gtsB, gtsC, gtsD, glk
Sulfuricurvum kujiense DSM 16994 ams, fruII-ABC, 1pfk, fba, tpi
Sulfurihydrogenibium azorense Az-Fu1 ams, ptsG-crr
Sulfurihydrogenibium subterraneum DSM 15120 ams, ptsG-crr
Sulfurimonas denitrificans DSM 1251 ams, fruII-ABC, 1pfk, fba, tpi
Sulfuritalea hydrogenivorans DSM 22779 sut, SUS, scrK, galU, pgmA
Sulfurivirga caldicuralii DSM 17737 sut, SUS, scrK, galU, pgmA
Synechococcus elongatus PCC 7942 thuE, thuF, thuG, thuK, ams, scrK, glk
Teredinibacter turnerae T7901 scrT, scrP, scrK, pgmA
Thauera aminoaromatica S2 sut, SUS, scrK, galU, pgmA
Thermithiobacillus tepidarius DSM 3134 sut, SUS, scrK, galU, pgmA
Thermocrinis albus DSM 14484 ams, fruII-ABC, 1pfk, fba, tpi
Thermodesulforhabdus norvegica DSM 9990 ams, fruII-ABC, 1pfk, fba, tpi
Thermomonospora curvata DSM 43183 ams, MFS-glucose, glk
Thermovibrio ammonificans HB-1 ams, fruII-ABC, 1pfk, fba, tpi
Thermus aquaticus YT-1 ams, gtsA, gtsB, gtsC, gtsD, glk
Thioalkalivibrio denitrificans ALJD sut, SUS, scrK, galU, pgmA
Thioalkalivibrio halophilus HL17 ams, Slc2a5, scrK
Thioalkalivibrio paradoxus ARh 1 ams, Slc2a5, scrK
Thioalkalivibrio thiocyanodenitrificans ARhD 1 sut, SUS, scrK, galU, pgmA
Thiohalomonas denitrificans HLD2 thuE, thuF, thuG, thuK, SUS, scrK, galU, pgmA
Thiohalospira halophila HL 3 sut, ams, scrK, glk
Thiomicrorhabdus arctica DSM 13458 ams, Slc2a5, scrK
Thiomicrorhabdus chilensis DSM 12352 ams, Slc2a5, scrK
Thiomicrospira cyclica ALM1 sut, SUS, scrK, galU, pgmA
Thiomicrospira microaerophila ASL8-2 sut, SUS, scrK, galU, pgmA
Thiomicrospira pelophila DSM 1534 sut, ams, scrK, glk
Thiothrix lacustris DSM 21227 sut, ams, scrK, glk
Tistlia consotensis USBA 355 ams, mglA, mglB, mglC, glk
Trichlorobacter lovleyi SZ ams, fruII-ABC, 1pfk, fba, tpi
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome ams, mglA, mglB, mglC, glk
Trichormus variabilis ATCC 29413 ams, frcA, frcB, frcC, scrK
Xanthobacter autotrophicus Py2 ams, frcA, frcB, frcC, scrK
Xenophilus azovorans DSM 13620 sut, SUS, scrK, galU, pgmA

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