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.
Links
Downloads
Related tools
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