GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Mesorhizobium ciceri biovar biserrulae WSM1271

Found 39 low-confidence and 44 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase MESCI_RS05450 MESCI_RS06630
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) MESCI_RS06170 MESCI_RS24305
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) MESCI_RS06145 MESCI_RS31055
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) MESCI_RS06150 MESCI_RS31060
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) MESCI_RS06150 MESCI_RS31060
arginine gbuA: guanidinobutyrase MESCI_RS02840 MESCI_RS22265
cellobiose cbp: cellobiose phosphorylase
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC MESCI_RS08880
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component MESCI_RS01590 MESCI_RS33060
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 MESCI_RS13050 MESCI_RS01605
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 MESCI_RS01600 MESCI_RS28130
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component MESCI_RS23340 MESCI_RS12995
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 MESCI_RS23335 MESCI_RS12990
D-alanine Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 MESCI_RS23330 MESCI_RS12985
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase MESCI_RS24660 MESCI_RS03935
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component MESCI_RS09010 MESCI_RS12435
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 MESCI_RS10300 MESCI_RS08985
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 MESCI_RS05470 MESCI_RS08980
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit MESCI_RS06665 MESCI_RS19000
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit MESCI_RS06670
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component MESCI_RS20490 MESCI_RS27410
fucose fucD: L-fuconate dehydratase MESCI_RS01485 MESCI_RS08470
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase MESCI_RS08470 MESCI_RS01485
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase MESCI_RS05880
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase MESCI_RS13040 MESCI_RS00555
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase MESCI_RS08350 MESCI_RS01535
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase MESCI_RS17130 MESCI_RS24275
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose lacE: lactose ABC transporter, substrate-binding component
lactose lacG: lactose ABC transporter, permease component 2 MESCI_RS11835 MESCI_RS07800
leucine liuC: 3-methylglutaconyl-CoA hydratase MESCI_RS30135 MESCI_RS09340
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine cadA: lysine decarboxylase MESCI_RS09615 MESCI_RS22175
lysine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase MESCI_RS05330 MESCI_RS29955
lysine patA: cadaverine aminotransferase MESCI_RS29885 MESCI_RS16850
mannose man-isomerase: D-mannose isomerase MESCI_RS24675
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
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase MESCI_RS30135 MESCI_RS23380
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase MESCI_RS00535 MESCI_RS23380
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase MESCI_RS05330 MESCI_RS29955
phenylacetate paaK: phenylacetate-CoA ligase MESCI_RS00605 MESCI_RS03565
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase MESCI_RS30135 MESCI_RS23380
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) MESCI_RS06145 MESCI_RS31055
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK MESCI_RS06170 MESCI_RS24305
phenylalanine maiA: maleylacetoacetate isomerase MESCI_RS17400 MESCI_RS21845
phenylalanine QDPR: 6,7-dihydropteridine reductase MESCI_RS13080
propionate putP: propionate transporter; proline:Na+ symporter
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) MESCI_RS06170 MESCI_RS24305
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) MESCI_RS06145 MESCI_RS31055
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) MESCI_RS06150 MESCI_RS31060
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) MESCI_RS06170 MESCI_RS24305
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) MESCI_RS06145 MESCI_RS31055
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) MESCI_RS06150 MESCI_RS31060
thymidine nupG: thymidine permease NupG/XapB
tryptophan andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb MESCI_RS13305
tryptophan andAc: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
tryptophan andAd: athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan kynB: kynurenine formamidase MESCI_RS26970 MESCI_RS19900
tryptophan mhpD: 2-hydroxypentadienoate hydratase MESCI_RS03390
tryptophan xylF: 2-hydroxymuconate semialdehyde hydrolase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase MESCI_RS17400 MESCI_RS21845
valine acdH: isobutyryl-CoA dehydrogenase MESCI_RS17130 MESCI_RS24275
valine mmsA: methylmalonate-semialdehyde dehydrogenase MESCI_RS06115 MESCI_RS03375
xylitol xdhA: xylitol dehydrogenase MESCI_RS01720 MESCI_RS26715

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