GapMind for catabolism of small carbon sources

 

trehalose catabolism

Analysis of pathway trehalose in 276 genomes

Genome Best path
Acidovorax caeni R-24608 treF, ptsG-crr
Actinokineospora bangkokensis 44EHW thuE, thuF, thuG, thuK, treF, glk
Actinomyces timonensis 7400942 treEIIA, treB, treC, glk
Algiphilus aromaticivorans DG1253 treF, SSS-glucose, glk
Algoriphagus aquaeductus T4 lacA, lacC, lacB, klh, SSS-glucose, glk
Algoriphagus machipongonensis PR1 lacA, lacC, lacB, klh, SSS-glucose, glk
Alicyclobacillus ferrooxydans TC-34 treF, gtsA, gtsB, gtsC, gtsD, glk
Alishewanella agri BL06 treF, MFS-glucose, glk
Alistipes indistinctus YIT 12060 BT2158, klh, MFS-glucose, glk
Alistipes shahii WAL 8301 BT2158, klh, MFS-glucose, glk
Alkalitalea saponilacus SC/BZ-SP2 BT2158, klh, SSS-glucose, glk
Amantichitinum ursilacus IGB-41 treF, gtsA, gtsB, gtsC, gtsD, glk
Amphibacillus jilinensis Y1 treEIIA, treB, treC, glk
Amphritea japonica JAMM 1866 treF, ptsG-crr
Amycolatopsis halophila YIM 93223 aglE, aglF, aglG, aglK, treF, glk
Amycolatopsis xylanica CPCC 202699 lpqY*, thuF, thuG, thuK, treF, glk
Aquimarina agarilytica ZC1 treF, SemiSWEET, glk
Aquimarina longa SW024 treF, ptsG-crr
Aquimarina macrocephali JAMB N27 treF, MFS-glucose, glk
Archaeoglobus sulfaticallidus PM70-1 treF, ptsG-crr
Arcticibacter svalbardensis MN12-7 treF, MFS-glucose, glk
Ardenticatena maritima 110S aglE, aglF, aglG, aglK, treF, glk
Arenimonas metalli CF5-1 treF, ptsG-crr
Arenitalea lutea P7-3-5 BT2158, klh, ptsG-crr
Azospirillum humicireducens SgZ-5 treF, mglA, mglB, mglC, glk
Azospirillum thiophilum BV-S treF, mglA, mglB, mglC, glk
Bacillus altitudinis 41KF2b treEIIA, treB, treC, glk
Bacillus coahuilensis m4-4 treEIIA, treB, treC, glk
Bacillus cytotoxicus NVH 391-98 treF, glcU', glk
Bacillus horneckiae 1P01SC TRET1, PsTP, pgmA, glk
Bacillus okhensis Kh10-101 treF, mglA, mglB, mglC, glk
Bacillus safensis FO-36b treEIIA, treB, treC, glk
Bacillus velezensis CBMB205 treEIIA, treB, treC, glk
Bacteroides clarus YIT 12056 treF, SSS-glucose, glk
Bacteroides faecis MAJ27 BT2158, klh, SSS-glucose, glk
Bacteroides fluxus YIT 12057 treF, MFS-glucose, glk
Bacteroides oleiciplenus YIT 12058 BT2158, klh, MFS-glucose, glk
Barnesiella intestinihominis YIT 11860 treF, MFS-glucose, glk
Belnapia rosea CPCC 100156 thuE, thuF, thuG, thuK, treF, glk
Bizionia argentinensis JUB59 treF, ptsG-crr
Bradyrhizobium diazoefficiens USDA110 treF, mglA, mglB, mglC, glk
Brevibacterium jeotgali SJ5-8 TRET1, PsTP, pgmA, glk
Brucella inopinata BO1 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Brucella microti CCM 4915 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Bryobacter aggregatus MPL3 TRET1, PsTP, pgmA, glk
Caldicellulosiruptor hydrothermalis 108 thuE, thuF, thuG, thuK, treP, pgmB, glk
Caldicellulosiruptor kronotskyensis 2002 thuE, thuF, thuG, thuK, treP, pgmB, glk
Carboxydothermus pertinax Ug1 treF, MFS-glucose, glk
Catellicoccus marimammalium M35/04/3 treF, manX, manY, manZ
Chromobacterium vaccinii MWU205 treEIIA, treB, treC, glk
Chryseobacterium angstadtii KM treF, SSS-glucose, glk
Chryseobacterium arthrosphaerae CC-VM-7 treF, MFS-glucose, glk
Chryseobacterium viscerum 687B-08 treF, MFS-glucose, glk
Cloacibacillus porcorum CL-84 TRET1, PsTP, pgmA, glk
Cobetia crustatorum JO1 thuE, thuF, thuG, thuK, treF, glk
Collimonas arenae Ter10 treF, mglA, mglB, mglC, glk
Collimonas pratensis Ter91 treF, gtsA, gtsB, gtsC, gtsD, glk
Collinsella tanakaei YIT 12063 treF, manX, manY, manZ
Coprobacter fastidiosus NSB1 treF, MFS-glucose, glk
Corynebacterium deserti GIMN1.010 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Corynebacterium frankenforstense ST18 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Corynebacterium lactis RW2-5 thuE, thuF, thuG, thuK, treP, pgmB, glk
Croceitalea dokdonensis DOKDO 023 BT2158, klh, SSS-glucose, glk
Cronobacter condimenti 1330 treF, mglA, mglB, mglC, glk
Cronobacter muytjensii ATCC 51329 treF, mglA, mglB, mglC, glk
Cronobacter universalis NCTC 9529 treF, mglA, mglB, mglC, glk
Desulfatitalea tepidiphila S28bF TRET1, PsTP, pgmA, glk
Desulfotomaculum hydrothermale Lam5 treF, ptsG-crr
Dethiosulfovibrio salsuginis USBA 82 treF, mglA, mglB, mglC, glk
Devosia chinhatensis IPL18 treF, mglA, mglB, mglC, glk
Devriesea agamarum IMP2 treF, MFS-glucose, glk
Dialister succinatiphilus YIT 11850 treF, ptsG-crr
Dietzia timorensis ID05-A0528 treF, MFS-glucose, glk
Dokdonella koreensis DS-123 treF, ptsG-crr
Domibacillus robiginosus WS 4628 treEIIA, treB, treC, glk
Duganella sacchari Sac-22 treF, MFS-glucose, glk
Dyadobacter tibetensis Y620-1 treF, SSS-glucose, glk
Dyella jiangningensis SBZ3-12 treF, MFS-glucose, glk
Endozoicomonas montiporae CL-33 treF, ptsG, crr
Enterococcus termitis LMG 8895 malF, malG, malK, malX, treP, pgmB, glk
Enterorhabdus caecimuris B7 treF, ptsG-crr
Epibacterium ulvae U95 treF, gtsA, gtsB, gtsC, gtsD, glk
Erythrobacter gangjinensis K7-2 treF, MFS-glucose, glk
Erythrobacter marinus HWDM-33 treF, MFS-glucose, glk
Ethanoligenens harbinense YUAN-3 treF, ptsG-crr
Fervidicella metallireducens AeB treF, ptsG-crr
Fibrella aestuarina BUZ 2 BT2158, klh, SSS-glucose, glk
Flammeovirga pacifica WPAGA1 treF, SSS-glucose, glk
Flaviramulus ichthyoenteri Th78 BT2158, klh, SSS-glucose, glk
Flavobacterium beibuense F44-8 treF, ptsG-crr
Flavobacterium glycines Gm-149 treF, SSS-glucose, glk
Flavobacterium sp. LM5 treF, ptsG-crr
Flavobacterium ummariense DS-12 treF, ptsG-crr
Frischella perrara PEB0191 treF, manX, manY, manZ
Galbibacter marinus ck-I2-15 BT2158, klh, MFS-glucose, glk
Gallaecimonas xiamenensis 3-C-1 treF, MFS-glucose, glk
Geobacter daltonii FRC-32 treF, ptsG-crr
Gillisia marina CBA3202 treF, ptsG-crr
Gracilibacillus halophilus YIM-C55.5 treEIIA, treB, treC, glk
Granulicella mallensis MP5ACTX8 treF, MFS-glucose, glk
Granulicella tundricola MP5ACTX9 treF, MFS-glucose, glk
Hafnia paralvei ATCC 29927 treEIIA, treB, treC, glk
Haladaptatus cibarius D43 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Halioglobus japonicus S1-36 TRET1, PsTP, pgmA, glk
Halobacillus alkaliphilus FP5 treEIIA, treB, treC, glk
Halococcus hamelinensis 100A6 treF, MFS-glucose, glk
Halomonas salina B6 thuE, thuF, thuG, thuK, treF, glk
Halomonas smyrnensis AAD6 thuE, thuF, thuG, thuK, treF, glk
Halomonas stevensii S18214 treF, gtsA, gtsB, gtsC, gtsD, glk
Halomonas titanicae BH1 treF, gtsA, gtsB, gtsC, gtsD, glk
Halomonas xinjiangensis TRM 0175 treF, gtsA, gtsB, gtsC, gtsD, glk
Halopiger salifodinae KCY07-B2 treF, gtsA, gtsB, gtsC, gtsD, glk
Halostagnicola larsenii XH-48 treF, MFS-glucose, glk
Haloterrigena daqingensis JX313 thuE, thuF, thuG, thuK, treF, glk
Herbaspirillum aquaticum IEH 4430 treF, mglA, mglB, mglC, glk
Hippea alviniae EP5-r treF, ptsG-crr
Hippea jasoniae Mar08-272r treF, ptsG-crr
Hoeflea phototrophica DFL-43 aglE, aglF, aglG, aglK, treF, glk
Hyphomicrobium nitrativorans NL23 treF, ptsG-crr
Imtechella halotolerans K1 treF, MFS-glucose, glk
Indibacter alkaliphilus LW1 lacA, lacC, lacB, klh, SSS-glucose, glk
Jannaschia aquimarina GSW-M26 treF, aglE', aglF', aglG', aglK', glk
Jeotgalibacillus soli P9 treEIIA, treB, treC, glk
Kangiella geojedonensis YCS-5 treF, ptsG-crr
Knoellia flava TL1 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Kocuria flava HO-9041 treF, MFS-glucose, glk
Kocuria turfanensis HO-9042 treF, MFS-glucose, glk
Laceyella sediminis RHA1 treF, ptsG-crr
Lacinutrix algicola AKS293 treF, ptsG-crr
Lacinutrix himadriensis E4-9a treF, ptsG-crr
Lacinutrix mariniflava AKS432 treF, ptsG-crr
Lactobacillus curieae CCTCC M 2011381 treEIIA, treB, trePP, pgmB
Lactobacillus delbrueckii ZN7a-9 treEIIA, treB, treC, glk
Lactobacillus hokkaidonensis LOOC260 treF, MFS-glucose, glk
Lactobacillus oryzae SG293 treF, glcU', glk
Lactobacillus pobuzihii E100301 treF, manX, manY, manZ
Lactobacillus shenzhenensis LY-73 malF, malG, malK, malX, treF, glk
Lactobacillus silagei IWT126 treF, MFS-glucose, glk
Leeuwenhoekiella blandensis MED217 BT2158, klh, SSS-glucose, glk
Lentibacillus jeotgali Grbi treF, MFS-glucose, glk
Limnohabitans curvus MWH-C5 treF, gtsA, gtsB, gtsC, gtsD, glk
Limnohabitans parvus II-B4 treF, gtsA, gtsB, gtsC, gtsD, glk
Listeria fleischmannii LU2006-1 treEIIA, treB, treC, glk
Luteimonas huabeiensis HB2 treF, MFS-glucose, glk
Luteipulveratus mongoliensis MN07-A0370 thuE, thuF, thuG, thuK, treP, pgmB, glk
Lutibaculum baratangense AMV1 treF, ptsG-crr
Lysobacter daejeonensis GH1-9 treF, SSS-glucose, glk
Magnetovibrio blakemorei MV-1 TRET1, PsTP, pgmA, glk
Marinicella litoralis KMM 3900 treF, ptsG-crr
Mariniradius saccharolyticus AK6 lacA, lacC, lacB, klh, SSS-glucose, glk
Marinobacter algicola DG893 treF, gtsA, gtsB, gtsC, gtsD, glk
Marinobacter guineae M3B treF, gtsA, gtsB, gtsC, gtsD, glk
Marinobacter psychrophilus 20041 TRET1, PsTP, pgmA, glk
Marinomonas arctica 328 treF, gtsA, gtsB, gtsC, gtsD, glk
Marivita geojedonensis DPG-138 treF, gtsA, gtsB, gtsC, gtsD, glk
Martelella endophytica YC6887 treF, aglE', aglF', aglG', aglK', glk
Megamonas funiformis YIT 11815 treF, MFS-glucose, glk
Mesorhizobium ciceri WSM1271 treF, aglE', aglF', aglG', aglK', glk
Methanobacterium arcticum M2 treF, ptsG-crr
Methanobacterium veterum MK4 treF, ptsG-crr
Methanocella arvoryzae MRE50 treF, ptsG-crr
Methanococcus aeolicus Nankai-3 treF, ptsG-crr
Methanoculleus horonobensis T10 TRET1, PsTP, pgmA, glk
Methanolinea tarda NOBI-1 treF, SemiSWEET, glk
Methanosarcina soligelidi SMA-21 treF, ptsG-crr
Methanospirillum lacunae Ki8-1 treF, SemiSWEET, glk
Methanospirillum stamsii Pt1 treF, SemiSWEET, glk
Methylibium petroleiphilum PM1 TRET1, PsTP, pgmA, glk
Methylobacterium gossipiicola Gh-105 TRET1, PsTP, pgmA, glk
Methylocapsa aurea KYG treF, MFS-glucose, glk
Methylotenera versatilis 301 treF, SemiSWEET, glk
Microbacterium profundi Shh49 treF, mglA, mglB, mglC, glk
Microvirga lotononidis WSM3557 treF, mglA, mglB, mglC, glk
Moritella dasanensis ArB 0140 treEIIA, treB, treC, glk
Mucilaginibacter gossypii Gh-67 lacA, lacC, lacB, klh, SSS-glucose, glk
Mucilaginibacter gossypiicola Gh-48 lacA, lacC, lacB, klh, SSS-glucose, glk
Mucilaginibacter mallensis MP1X4 lacA, lacC, lacB, klh, SSS-glucose, glk
Nafulsella turpanensis ZLM-10 treF, MFS-glucose, glk
Natronomonas moolapensis 8.8.11 treF, ptsG-crr
Nautilia profundicola AmH treF, ptsG-crr
Neiella marina J221 treF, ptsG, crr
Neptunomonas antarctica S3-22 treF, ptsG-crr
Nocardioides daejeonensis MJ31 treF, MFS-glucose, glk
Nocardioides dokdonensis FR1436 thuE, thuF, thuG, thuK, treF, glk
Nocardiopsis baichengensis YIM 90130 treF, mglA, mglB, mglC, glk
Nocardiopsis gilva YIM 90087 treF, MFS-glucose, glk
Novosphingobium barchaimii LL02 treF, MFS-glucose, glk
Novosphingobium fuchskuhlense FNE08-7 treF, MFS-glucose, glk
Novosphingobium lindaniclasticum LE124 treF, MFS-glucose, glk
Oceanisphaera arctica V1-41 treF, ptsG, crr
Ochrobactrum rhizosphaerae PR17 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Ochrobactrum thiophenivorans DSM 7216 treF, mglA, mglB, mglC, glk
Oscillibacter ruminantium GH1 treF, mglA, mglB, mglC, glk
Paenisporosarcina indica PN2 treF, ptsG-crr
Palaeococcus pacificus DY20341 treF, ptsG-crr
Paludibacter propionicigenes WB4 treF, SemiSWEET, glk
Pandoraea thiooxydans ATSB16 treF, MFS-glucose, glk
Pantoea rwandensis LMG 26275 treF, mglA, mglB, mglC, glk
Pedobacter arcticus A12 treF, MFS-glucose, glk
Photobacterium gaetbulicola Gung47 treEIIA, treB, treC, glk
Photobacterium jeanii R-40508 treEIIA, treB, treC, glk
Phyllobacterium brassicacearum STM 196 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Phyllobacterium endophyticum PEPV15 treF, gtsA, gtsB, gtsC, gtsD, glk
Phyllobacterium leguminum ORS 1419 aglE, aglF, aglG, aglK, PsTP, pgmA, glk
Planktomarina temperata RCA23 treF, mglA, mglB, mglC, glk
Planococcus halocryophilus Or1 treF, ptsG-crr
Pleomorphomonas diazotrophica R5-392 thuE, thuF, thuG, thuK, treP, pgmB, glk
Polaribacter dokdonensis DSW-5 treF, MFS-glucose, glk
Pontibacillus litoralis JSM 072002 treF, ptsG-crr
Pontibacter lucknowensis DM9 treF, MFS-glucose, glk
Pontibacter ramchanderi LP43 treF, MFS-glucose, glk
Pontimonas salivibrio CL-TW6 treF, mglA, mglB, mglC, glk
Porphyrobacter dokdonensis DSW-74 treF, MFS-glucose, glk
Pseudoalteromonas arctica A 37-1-2 treF, MFS-glucose, glk
Pseudomonas baetica a390 treF, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas litoralis 2SM5 treF, ptsG-crr
Pseudomonas taeanensis MS-3 treF, gtsA, gtsB, gtsC, gtsD, glk
Pseudovibrio axinellae Ad2 treF, gtsA, gtsB, gtsC, gtsD, glk
Psychrobacter arcticus 273-4 treF, ptsG-crr
Psychrobacter cryohalolentis K5 treF, ptsG-crr
Psychromonas ingrahamii 37 treEIIA, treB, treC, glk
Psychromonas ossibalaenae JAMM 0738 treEIIA, treB, treC, glk
Rhizobium freirei PRF 81 treF, gtsA, gtsB, gtsC, gtsD, glk
Rhizobium grahamii CCGE 502 treF, aglE', aglF', aglG', aglK', glk
Rhizobium subbaraonis JC85 treF, aglE', aglF', aglG', aglK', glk
Rhodanobacter denitrificans 2APBS1 treF, MFS-glucose, glk
Rhodobacter johrii JA192 treF, aglE', aglF', aglG', aglK', glk
Rhodobacter maris JA276 treF, aglE', aglF', aglG', aglK', glk
Rhodobacter ovatus JA234 TRET1, PsTP, pgmA, glk
Rhodobacter viridis JA737 treF, aglE', aglF', aglG', aglK', glk
Rhodococcus qingshengii djl-6-2 lpqY, thuF, thuG, thuK, treF, glk
Rhodopseudomonas pseudopalustris DSM 123 treF, ptsG-crr
Roseateles aquatilis CCUG 48205 treF, gtsA, gtsB, gtsC, gtsD, glk
Roseivirga spongicola UST030701-084 BT2158, klh, MFS-glucose, glk
Rubrivirga marina SAORIC-28 treF, MFS-glucose, glk
Ruegeria conchae TW15 treF, gtsA, gtsB, gtsC, gtsD, glk
Saccharomonospora marina XMU15 thuE, thuF, thuG, thuK, treF, glk
Salinicoccus carnicancri Crm treEIIA, treB, treC, glk
Serinicoccus profundi MCCC 1A05965 treF, MFS-glucose, glk
Shewanella halifaxensis HAW-EB4 treF, SSS-glucose, glk
Skermanella stibiiresistens SB22 treF, mglA, mglB, mglC, glk
Snodgrassella alvi wkB2 treF, ptsG-crr
Sphaerochaeta globosa Buddy treF, mglA, mglB, mglC, glk
Sphaerochaeta pleomorpha Grapes treF, mglA, mglB, mglC, glk
Sphingobium baderi LL03 treF, MFS-glucose, glk
Sphingobium czechense LL01 treF, MFS-glucose, glk
Sphingobium quisquiliarum P25 treF, MFS-glucose, glk
Sphingomonas histidinilytica UM2 TRET1, PsTP, pgmA, glk
Sphingomonas indica Dd16 treF, ptsG-crr
Sphingomonas laterariae LNB2 treF, MFS-glucose, glk
Sphingopyxis indica DS15 treF, MFS-glucose, glk
Sphingopyxis terrae UI2 treF, MFS-glucose, glk
Sporolactobacillus vineae SL153 thuE, thuF, thuG, thuK, treP, pgmB, glk
Streptacidiphilus oryzae TH49 treF, MFS-glucose, glk
Streptococcus anginosus CCUG 39159 treEIIA, treB, treC, glk
Streptococcus massiliensis 4401825 treEIIA, treB, treC, glk
Streptococcus oralis 7747 treF, manX, manY, manZ
Streptococcus oralis AZ_3a treF, manX, manY, manZ
Streptomyces kebangsaanensis SUK12 treF, mglA, mglB, mglC, glk
Succinatimonas hippei YIT 12066 treF, mglA, mglB, mglC, glk
Sulfurimonas gotlandica GD1 treF, ptsG-crr
Tatumella morbirosei LMG 23360 treF, mglA, mglB, mglC, glk
Thauera humireducens SgZ-1 TRET1, PsTP, pgmA, glk
Thermoactinomyces daqus H-18 treEIIA, treB, treC, glk
Thermobifida halotolerans YIM 90462 treF, MFS-glucose, glk
Thermodesulfovibrio aggregans TGE-P1 treF, SemiSWEET, glk
Thermophagus xiamenensis HS1 BT2158, klh, SSS-glucose, glk
Thermovenabulum gondwanense R270 TRET1, PsTP, pgmA, glk
Thioclava dalianensis DLFJ1-1 treF, aglE', aglF', aglG', aglK', glk
Thiohalospira halophila HL 3 TRET1, PsTP, pgmA, glk
Tistlia consotensis USBA 355 treF, mglA, mglB, mglC, glk
Vagococcus penaei CD276 treEIIA, treB, treC, glk
Verminephrobacter eiseniae EF01-2 treF, mglA, mglB, mglC, glk
Weissella oryzae SG25 treF, manX, manY, manZ
Williamsia sterculiae CPCC 203464 lpqY, thuF, thuG, thuK, treF, glk
Yersinia intermedia Y228 treEIIA, treB, treC, 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