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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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