As text, or see rules and steps
# Rhamnose utilization in GapMind is based on MetaCyc pathway # I via L-rhamnulose 1-phosphate aldolase (metacyc:RHAMCAT-PWY), # pathway II via 2-keto-3-deoxy-L-rhamnonate aldolase (metacyc:PWY-6713), # and pathway III via 2,4-diketo-3-deoxyrhamnonate hydrolase (metacyc:PWY-6714). # Fitness data shows that the (distant) homolog in Bacteroides thetaiotaomicron (BT3765, Q8A1A1) is also # a rhamnose transporter rhaT L-rhamnose:H+ symporter RhaT curated:SwissProt::P27125 uniprot:Q8A1A1 # Transporters were identified usiung: # query: transporter:L-rhamnose:rhamnose:L-rhamnofuranose:L-rhamnopyranose:CPD-16564:CPD-16565:CPD0-1112:CPD-15405 rhamnose-transport: rhaT # 4-part ABC transporter rhaPQST. # In TCDB, the rhamnose transporter of Rhizobium leguminosarum is described as rhaSTP # but rhaQ (Q7BSH2_RHILT) is also probably part of this system. # The comment in TCDB also speculates about group translocation, because the R. leguminosarum # system requires the rhamnose/rhamnulose kinase rhaK for activity; but # in Sinorhizobium meliloti, which has a similar system, # the rhaK protein has rhamnulokinase activity only # (Rivers 2015, URL:https://mspace.lib.umanitoba.ca/handle/1993/30289). rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) curated:TCDB::Q7BSH3 rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) uniprot:Q7BSH2 rhaS L-rhamnose ABC transporter, substrate-binding component RhaS curated:TCDB::Q7BSH5 # Because of the one-component transporter rhaT, the ATPase component is named rhaT' in GapMind. rhaT' L-rhamnose ABC transporter, ATPase component RhaT curated:TCDB::Q7BSH4 rhamnose-transport: rhaP rhaQ rhaS rhaT' # Fitness data suggests Echvi_1617 is the rhamnose transporter. # It is probably Na+ dependent, but this is uncertain. Echvi_1617 L-rhamnose transporter uniprot:L0FX46 rhamnose-transport: Echvi_1617 # In Burkholderia phytofirmans PsJN, a 3-part ABC transporter is involved # in utilization of L-rhamnose, L-fucose, and xylitol BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component uniprot:B2T9W0 BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component uniprot:B2T9V9 BPHYT_RS34240 L-rhamnose ABC transporter, permease component uniprot:B2T9V8 rhamnose-transport: BPHYT_RS34250 BPHYT_RS34245 BPHYT_RS34240 rhaM L-rhamnose mutarotase EC:5.1.3.32 rhaA L-rhamnose isomerase EC:5.3.1.14 rhaB L-rhamnulokinase EC:2.7.1.5 # BT3766 (Q8A1A0) was confirmed by fitness data rhaD rhamnulose 1-phosphate aldolase EC:4.1.2.19 uniprot:Q8A1A0 import fructose.steps:tpi # triose-phsophate isomerase # The EC number is for the NAD dependent reaction. # There's also a NADP dependent reaction, sometimes given this EC, sometimes not. aldA lactaldehyde dehydrogenase EC:1.2.1.22 ignore_other:lactaldehyde dehydrogenase # BT3767 (Q8A199) was confirmed by fitness data fucO L-lactaldehyde reductase EC:1.1.1.77 uniprot:Q8A199 # Lactaldehyde might be oxidized to # lactate and secreted (or oxidized to pyruvate); or, it might be # reduced to propane-1,2-diol and secreted. lactaldehyde-conversion: aldA lactaldehyde-conversion: fucO # In pathway I, the mutarotase rhaM forms # beta-rhamnopyranose, isomerase rhaA forms rhamnulofuranose, kinase rhaB # forms rhamnulose 1-phosphate, aldolase rhaD forms (S)-lactaldehyde and # glycerone phosphate, and tpi converts glycerone phosphate to # glyceraldehyde 3-phosphate. all: rhamnose-transport rhaM rhaA rhaB rhaD tpi lactaldehyde-conversion # The rhamnofuranose dehydrogenase may be either NADH or NADPH dependent, or use either LRA1 L-rhamnofuranose dehydrogenase EC:1.1.1.378 EC:1.1.1.173 EC:1.1.1.377 LRA2 L-rhamnono-gamma-lactonase EC:3.1.1.65 # Ignore BPHYT_RS34235, a putative accessory domain LRA3 L-rhamnonate dehydratase EC:4.2.1.90 ignore:reanno::BFirm:BPHYT_RS34235 LRA4 2-keto-3-deoxy-L-rhamnonate aldolase EC:4.1.2.53 # In pathway II, the 1-dehydrogenase LRA1 forms L-rhamnono-1,4-lactone, # the lactonase LRA2 forms L-rhamnonate, the dehydratase LRA3 forms # 2-dehydro-3-deoxy-L-rhamnonate, and the aldolase LRA4 forms pyruvate and # lactaldehyde. all: rhamnose-transport LRA1 LRA2 LRA3 LRA4 lactaldehyde-conversion # The enzyme from Sphingomonas strain SKA58 is Q1NEI6 not Q1NEI7; there is an error in MetaCyc. # Q1NEI6 is annotated correctly in other resources LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase EC:1.1.1.401 ignore:metacyc::MONOMER-16233 # EC:3.7.1.26 has been assigned but not linked to the characterized protein, which is # EAT09363.1 or metacyc:MONOMER-16233 (PMID:19187228) -- but MONOMER-16233 is misannotated as # a dehydrogenase. # And, ignore uniprot:Q39BA7, which is very similar to LRA6 from Burkholderia phytofirmans PsJN # but is reported to be a ureidoglycolate lyase (PMID:14506266). LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase curated:metacyc::MONOMER-16233 term:L-2,4-diketo-3-deoxyrhamnonate hydrolase term:2,4-diketo-3-deoxy-L-rhamnonate hydrolase EC:3.7.1.26 ignore:SwissProt::Q39BA7 # In pathway III, rhamnose is also oxidized and dehydrated to # 2-dehydro-3-deoxy-L-rhamnonate, but then, dehydrogenase LRA5 forms # 2,4-didehydro-3-deoxy-L-rhamnonate and hydrolase LRA6 forms L-lactate # and pyruvate. all: rhamnose-transport LRA1 LRA2 LRA3 LRA5 LRA6
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:
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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