GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Herbaspirillum seropedicae SmR1

Found 34 low-confidence and 46 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaC: 4-carboxymuconolactone decarboxylase HSERO_RS19935 HSERO_RS06525
4-hydroxybenzoate pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase HSERO_RS19990 HSERO_RS20660
4-hydroxybenzoate pcaH: protocatechuate 3,4-dioxygenase, alpha subunit HSERO_RS19925 HSERO_RS19920
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK HSERO_RS05600 HSERO_RS06575
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) HSERO_RS08290 HSERO_RS14710
arginine braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC HSERO_RS08270 HSERO_RS17350
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) HSERO_RS08275 HSERO_RS05960
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) HSERO_RS08280 HSERO_RS05965
arginine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) HSERO_RS08285 HSERO_RS20055
arginine braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) HSERO_RS08290 HSERO_RS05975
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HSERO_RS05835 HSERO_RS00320
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 HSERO_RS19335 HSERO_RS05830
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 HSERO_RS10770 HSERO_RS11445
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component HSERO_RS10775 HSERO_RS21615
citrulline arcC: carbamate kinase
D-alanine AZOBR_RS08235: D-alanine ABC transporter, permease component 1 HSERO_RS08275 HSERO_RS05960
D-alanine AZOBR_RS08240: D-alanine ABC transporter, permease component 2 HSERO_RS08280 HSERO_RS00890
D-alanine AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 HSERO_RS08285 HSERO_RS05970
D-alanine AZOBR_RS08250: D-alanine ABC transporter, ATPase component 2 HSERO_RS08290 HSERO_RS05975
D-alanine AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component HSERO_RS08270 HSERO_RS00870
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 HSERO_RS01420 HSERO_RS00265
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter HSERO_RS05805 HSERO_RS05735
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter HSERO_RS05805 HSERO_RS05735
deoxyribose drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit HSERO_RS06620 HSERO_RS16320
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component HSERO_RS16735 HSERO_RS22390
glucosamine nagK: N-acetylglucosamine kinase HSERO_RS17870 HSERO_RS22755
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucosamine SMc02869: N-acetylglucosamine ABC transporter, ATPase component HSERO_RS16715 HSERO_RS22750
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate uxuL: D-glucaro-1,5-lactonase UxuL or UxuF HSERO_RS15795 HSERO_RS19370
glutamate gdhA: glutamate dehydrogenase, NAD-dependent HSERO_RS19260
histidine hutG': N-formylglutamate amidohydrolase
histidine hutH: histidine ammonia-lyase HSERO_RS22680 HSERO_RS18505
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose lacP: lactose permease LacP
lysine gcdG: succinyl-CoA:glutarate CoA-transferase HSERO_RS18350 HSERO_RS14050
lysine gcdH: glutaryl-CoA dehydrogenase HSERO_RS23440 HSERO_RS04640
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase HSERO_RS05420 HSERO_RS17580
lysine patD: 5-aminopentanal dehydrogenase HSERO_RS05645 HSERO_RS09465
maltose susB: alpha-glucosidase (maltase) HSERO_RS20525 HSERO_RS11645
mannitol mt2d: mannitol 2-dehydrogenase HSERO_RS02215 HSERO_RS17015
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE HSERO_RS02190
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) HSERO_RS02195 HSERO_RS16725
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) HSERO_RS02200 HSERO_RS04860
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG HSERO_RS02210 HSERO_RS22750
NAG nagK: N-acetylglucosamine kinase HSERO_RS17870 HSERO_RS22755
NAG SMc02869: N-acetylglucosamine ABC transporter, ATPase component HSERO_RS16715 HSERO_RS22750
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB HSERO_RS21380 HSERO_RS12755
propionate putP: propionate transporter; proline:Na+ symporter
putrescine patA: putrescine aminotransferase (PatA/SpuC) HSERO_RS05635 HSERO_RS23240
putrescine patD: gamma-aminobutyraldehyde dehydrogenase HSERO_RS19755 HSERO_RS09465
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
sucrose ams: sucrose hydrolase (invertase)
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) HSERO_RS08290 HSERO_RS14710
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine deoA: thymidine phosphorylase DeoA HSERO_RS07175
thymidine deoB: phosphopentomutase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase HSERO_RS00970 HSERO_RS11645
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA HSERO_RS06550 HSERO_RS06720
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB HSERO_RS06555
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC HSERO_RS06560 HSERO_RS18275
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan catC: muconolactone isomerase HSERO_RS06530
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase HSERO_RS05590 HSERO_RS18245
tryptophan pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase HSERO_RS19990 HSERO_RS20660
valine bch: 3-hydroxyisobutyryl-CoA hydrolase HSERO_RS01610 HSERO_RS20665
valine mmsB: 3-hydroxyisobutyrate dehydrogenase HSERO_RS15390 HSERO_RS21160
xylose xylC: xylonolactonase HSERO_RS19370 HSERO_RS05225

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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