GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Rhizobium etli CFN 42

Found 32 low-confidence and 37 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP RHE_RS20930
4-hydroxybenzoate pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase RHE_RS25075 RHE_RS20545
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RHE_RS16985 RHE_RS15820
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RHE_RS17010 RHE_RS25480
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RHE_RS17000 RHE_RS25470
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC RHE_RS18325
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component RHE_RS23640 RHE_RS10945
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 RHE_RS30300 RHE_RS24430
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 RHE_RS30305 RHE_RS23650
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component RHE_RS12350 RHE_RS23645
citrulline arcC: carbamate kinase
D-serine cycA: D-serine:H+ symporter CycA RHE_RS25845
D-serine dsdA: D-serine ammonia-lyase RHE_RS18080 RHE_RS10385
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component RHE_RS00950
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 RHE_RS00960 RHE_RS22540
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 RHE_RS00965 RHE_RS22545
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase RHE_RS23955 RHE_RS29990
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter RHE_RS24105
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme RHE_RS23475
deoxyribose deoP: deoxyribose transporter
fucose fdh: L-fucose 1-dehydrogenase RHE_RS02500 RHE_RS28605
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component RHE_RS26590 RHE_RS12255
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component RHE_RS02490
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase RHE_RS28415 RHE_RS27620
galacturonate gli: D-galactarolactone isomerase
gluconate gntA: gluconate TRAP transporter, small permease component RHE_RS23920
gluconate gntB: gluconate TRAP transporter, large permease component RHE_RS23925 RHE_RS26780
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase RHE_RS28415 RHE_RS27620
lactose lacE: lactose ABC transporter, substrate-binding component
lactose lacG: lactose ABC transporter, permease component 2 RHE_RS22755 RHE_RS23250
leucine liuC: 3-methylglutaconyl-CoA hydratase RHE_RS01800 RHE_RS08795
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit RHE_RS23160 RHE_RS11415
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine hisP: L-lysine ABC transporter, ATPase component HisP RHE_RS11715 RHE_RS23640
lysine lysN: 2-aminoadipate transaminase RHE_RS15340 RHE_RS23780
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase RHE_RS04520 RHE_RS04070
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) RHE_RS18820 RHE_RS23355
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 RHE_RS28460
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase RHE_RS01800 RHE_RS23495
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase RHE_RS02825 RHE_RS19395
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase RHE_RS01800
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) RHE_RS17010 RHE_RS25480
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK RHE_RS16985 RHE_RS15820
phenylalanine QDPR: 6,7-dihydropteridine reductase
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RHE_RS16985 RHE_RS15820
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RHE_RS17010 RHE_RS25480
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RHE_RS17000 RHE_RS25470
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RHE_RS16985 RHE_RS15820
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RHE_RS17010 RHE_RS25480
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RHE_RS17000 RHE_RS25470
thymidine nupG: thymidine permease NupG/XapB
tryptophan aroP: tryptophan:H+ symporter AroP RHE_RS25845
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) RHE_RS25845
valine bch: 3-hydroxyisobutyryl-CoA hydrolase RHE_RS02885 RHE_RS01800
valine mmsA: methylmalonate-semialdehyde dehydrogenase RHE_RS03695 RHE_RS05810
xylitol PS417_12055: xylitol ABC transporter, substrate-binding component RHE_RS12260 RHE_RS13525
xylitol PS417_12065: xylitol ABC transporter, ATPase component RHE_RS20390 RHE_RS06210

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