GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Rhizobium leguminosarum bv. trifolii WSM1325

Found 32 low-confidence and 32 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP RLEG_RS20920 RLEG_RS14065
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RLEG_RS16390 RLEG_RS15300
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RLEG_RS16415 RLEG_RS27550
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RLEG_RS16405 RLEG_RS27560
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC RLEG_RS17955
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component RLEG_RS34600 RLEG_RS28480
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 RLEG_RS28485 RLEG_RS11325
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 RLEG_RS34590 RLEG_RS28490
citrulline arcC: carbamate kinase
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase RLEG_RS17685 RLEG_RS28165
deoxyinosine H281DRAFT_01112: deoxynucleoside transporter, permease component 2 RLEG_RS26310 RLEG_RS26350
deoxyinosine H281DRAFT_01113: deoxynucleoside transporter, ATPase component RLEG_RS26305 RLEG_RS32730
deoxyinosine H281DRAFT_01115: deoxynucleoside transporter, permease component 1 RLEG_RS26315 RLEG_RS03525
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase RLEG_RS15460 RLEG_RS18620
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter RLEG_RS29595
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme RLEG_RS34775
deoxyribose deoP: deoxyribose transporter
fucose fdh: L-fucose 1-dehydrogenase RLEG_RS00805 RLEG_RS31245
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component RLEG_RS23605 RLEG_RS06905
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component RLEG_RS00795
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate udh: D-galacturonate dehydrogenase RLEG_RS25645
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) RLEG_RS25640 RLEG_RS02700
gluconate gntT: gluconate:H+ symporter GntT
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase RLEG_RS15350 RLEG_RS01480
glucuronate uxaC: D-glucuronate isomerase RLEG_RS21585
lactose lacE: lactose ABC transporter, substrate-binding component
lactose lacG: lactose ABC transporter, permease component 2 RLEG_RS33210 RLEG_RS25055
leucine liuC: 3-methylglutaconyl-CoA hydratase RLEG_RS23030 RLEG_RS26045
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit RLEG_RS35165 RLEG_RS10295
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine hisP: L-lysine ABC transporter, ATPase component HisP RLEG_RS34600 RLEG_RS08715
lysine lysN: 2-aminoadipate transaminase RLEG_RS14800 RLEG_RS34460
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase RLEG_RS02945
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) RLEG_RS18520 RLEG_RS25765
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E RLEG_RS24055
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase RLEG_RS26045 RLEG_RS23030
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase RLEG_RS01235 RLEG_RS19090
phenylacetate paaK: phenylacetate-CoA ligase RLEG_RS23870
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase RLEG_RS23030 RLEG_RS26045
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) RLEG_RS16415 RLEG_RS23810
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK RLEG_RS16390 RLEG_RS15300
phenylalanine QDPR: 6,7-dihydropteridine reductase RLEG_RS27200
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RLEG_RS16390 RLEG_RS15300
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RLEG_RS16415 RLEG_RS27550
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RLEG_RS16405 RLEG_RS27560
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RLEG_RS16390 RLEG_RS15300
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RLEG_RS16415 RLEG_RS27550
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RLEG_RS16405 RLEG_RS27560
thymidine nupG: thymidine permease NupG/XapB
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine mmsA: methylmalonate-semialdehyde dehydrogenase RLEG_RS02115 RLEG_RS04395

Confidence: high confidence medium confidence low confidence

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