GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Sinorhizobium fredii NGR234

Found 19 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 NGR_RS27720
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) NGR_RS23720 NGR_RS14075
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) NGR_RS23745 NGR_RS28280
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) NGR_RS23740 NGR_RS10930
asparagine ans: asparaginase NGR_RS19420 NGR_RS14865
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC NGR_RS09900 NGR_RS03725
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component NGR_RS12355 NGR_RS01720
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 NGR_RS12340 NGR_RS01705
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 NGR_RS01710 NGR_RS12345
D-serine cycA: D-serine:H+ symporter CycA NGR_RS11085
D-serine dsdA: D-serine ammonia-lyase NGR_RS09375 NGR_RS09445
deoxyinosine H281DRAFT_01112: deoxynucleoside transporter, permease component 2 NGR_RS05500 NGR_RS00535
deoxyinosine H281DRAFT_01113: deoxynucleoside transporter, ATPase component NGR_RS19930 NGR_RS05495
deoxyinosine H281DRAFT_01114: deoxynucleoside transporter, substrate-binding component NGR_RS05490 NGR_RS12580
deoxyinosine H281DRAFT_01115: deoxynucleoside transporter, permease component 1 NGR_RS05505 NGR_RS02105
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase NGR_RS09535 NGR_RS13555
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter NGR_RS09750
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme NGR_RS21970 NGR_RS14520
deoxyribose deoP: deoxyribose transporter
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component NGR_RS27955
galactose dgoD: D-galactonate dehydratase NGR_RS23200 NGR_RS13535
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase NGR_RS06830
galacturonate gli: D-galactarolactone isomerase
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase NGR_RS06830
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase NGR_RS10015 NGR_RS05525
lactose dgoD: D-galactonate dehydratase NGR_RS23200 NGR_RS13535
lysine hisP: L-lysine ABC transporter, ATPase component HisP NGR_RS12355 NGR_RS17840
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) NGR_RS23515 NGR_RS09945
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase NGR_RS24175 NGR_RS12210
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine ARO10: phenylpyruvate decarboxylase
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) NGR_RS23745 NGR_RS10925
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK NGR_RS23720 NGR_RS14075
phenylalanine paaH: 3-hydroxyadipyl-CoA dehydrogenase NGR_RS24175 NGR_RS12210
phenylalanine pad-dh: phenylacetaldehyde dehydrogenase NGR_RS02250 NGR_RS14395
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) NGR_RS23720 NGR_RS14075
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) NGR_RS23745 NGR_RS28280
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) NGR_RS23740 NGR_RS10930
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) NGR_RS23720 NGR_RS14075
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) NGR_RS23745 NGR_RS28280
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) NGR_RS23740 NGR_RS10930
thymidine nupG: thymidine permease NupG/XapB
tryptophan aroP: tryptophan:H+ symporter AroP NGR_RS11085
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) NGR_RS11085
tyrosine maiA: maleylacetoacetate isomerase NGR_RS26110 NGR_RS27495
valine acdH: isobutyryl-CoA dehydrogenase NGR_RS10015 NGR_RS05525
valine bch: 3-hydroxyisobutyryl-CoA hydrolase NGR_RS10010 NGR_RS29675
valine mmsA: methylmalonate-semialdehyde dehydrogenase NGR_RS13065 NGR_RS14830
valine mmsB: 3-hydroxyisobutyrate dehydrogenase NGR_RS10005 NGR_RS09755
xylitol xdhA: xylitol dehydrogenase NGR_RS10700 NGR_RS09240

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