GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Caulobacter crescentus NA1000

Found 74 low-confidence and 34 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) CCNA_00206 CCNA_02488
4-hydroxybenzoate pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) CCNA_02489 CCNA_00207
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK CCNA_02495
alanine snatA: L-alanine symporter SnatA CCNA_00105
arabinose araE: L-arabinose:H+ symporter CCNA_00857
arabinose xacC: L-arabinono-1,4-lactonase CCNA_00863 CCNA_01882
arabinose xacD: L-arabinonate dehydratase CCNA_01488 CCNA_00862
arginine adiA: arginine decarboxylase (AdiA/SpeA)
arginine gabT: gamma-aminobutyrate transaminase CCNA_03233 CCNA_03245
arginine puuB: gamma-glutamylputrescine oxidase CCNA_03229
arginine rocE: L-arginine permease
asparagine ans: asparaginase CCNA_00278 CCNA_00096
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component CCNA_01506 CCNA_02751
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 CCNA_01507
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 CCNA_01507
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component CCNA_01508
citrulline citrullinase: putative citrullinase CCNA_00212
citrulline gabT: gamma-aminobutyrate transaminase CCNA_03233 CCNA_03245
citrulline odc: L-ornithine decarboxylase CCNA_00365
citrulline puuB: gamma-glutamylputrescine oxidase CCNA_03229
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase CCNA_03500 CCNA_03322
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 CCNA_02112 CCNA_03203
deoxyinosine deoB: phosphopentomutase CCNA_02347
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC CCNA_02171
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CCNA_01892 CCNA_03172
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter CCNA_02439
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase CCNA_03243 CCNA_03695
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose dgoD: D-galactonate dehydratase CCNA_01488 CCNA_00862
galactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) CCNA_00863 CCNA_01882
galactose HP1174: Na+-dependent galactose transporter CCNA_01159
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase CCNA_01557
gluconate gntK: D-gluconate kinase CCNA_03103
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX CCNA_00575
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate uxaC: D-glucuronate isomerase CCNA_01557
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF CCNA_01572
isoleucine Bap2: L-isoleucine permease Bap2
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuE: hydroxymethylglutaryl-CoA lyase CCNA_00500
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase CCNA_03233 CCNA_02326
lysine lysN: 2-aminoadipate transaminase CCNA_01603 CCNA_02244
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase CCNA_03500
mannitol mt2d: mannitol 2-dehydrogenase CCNA_01554 CCNA_03491
mannitol PLT5: polyol transporter PLT5
mannose manP: mannose PTS system, EII-CBA components
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 CCNA_00006 CCNA_02658
phenylacetate paaK: phenylacetate-CoA ligase CCNA_01382 CCNA_03292
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase CCNA_02658 CCNA_00006
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase CCNA_03233 CCNA_03245
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) CCNA_03238
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) CCNA_03236
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) CCNA_03239
putrescine puuB: gamma-glutamylputrescine oxidase CCNA_03229
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase CCNA_03243 CCNA_03695
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter CCNA_00105
sorbitol sdh: sorbitol dehydrogenase CCNA_01892 CCNA_01345
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) CCNA_03462 CCNA_03463
threonine snatA: L-threonine transporter snatA CCNA_00105
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase CCNA_02347
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase CCNA_02368
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine Bap2: L-valine permease Bap2
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase CCNA_03124

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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