Potential Gaps in catabolism of small carbon sources in Pseudovibrio axinellae Ad2
Found 57 low-confidence and 62 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ | PsAD2_RS05440 | |
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | PsAD2_RS06250 | |
| 4-hydroxybenzoate | pcaC: 4-carboxymuconolactone decarboxylase | | |
| 4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | | |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | PsAD2_RS08175 | PsAD2_RS01745 |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | PsAD2_RS00855 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | PsAD2_RS02810 | PsAD2_RS07425 |
| arabinose | araE: L-arabinose:H+ symporter | PsAD2_RS21425 | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | PsAD2_RS20325 | PsAD2_RS06355 |
| arabinose | xacC: L-arabinono-1,4-lactonase | PsAD2_RS03450 | |
| arabinose | xacD: L-arabinonate dehydratase | PsAD2_RS04990 | |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | PsAD2_RS02835 | |
| asparagine | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | PsAD2_RS01035 | |
| asparagine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | PsAD2_RS01045 | PsAD2_RS20750 |
| asparagine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | PsAD2_RS01040 | |
| aspartate | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | PsAD2_RS01035 | |
| aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | PsAD2_RS01045 | PsAD2_RS20750 |
| aspartate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | PsAD2_RS01040 | |
| cellobiose | bgl: cellobiase | PsAD2_RS11455 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | PsAD2_RS01050 | PsAD2_RS05610 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | PsAD2_RS20755 | PsAD2_RS13415 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | PsAD2_RS13420 | PsAD2_RS20750 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | PsAD2_RS01035 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | PsAD2_RS01040 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | PsAD2_RS01050 | PsAD2_RS05610 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | PsAD2_RS03350 | PsAD2_RS16680 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | PsAD2_RS00800 | PsAD2_RS18230 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | PsAD2_RS00840 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | glcP: fructose:H+ symporter GlcP | PsAD2_RS21425 | PsAD2_RS22100 |
| fructose | scrK: fructokinase | PsAD2_RS05040 | PsAD2_RS21780 |
| fucose | aldA: lactaldehyde dehydrogenase | PsAD2_RS08865 | PsAD2_RS20650 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | PsAD2_RS05045 | |
| 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 | galE: UDP-glucose 4-epimerase | PsAD2_RS10675 | PsAD2_RS21375 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galactose | pgmA: alpha-phosphoglucomutase | PsAD2_RS05080 | PsAD2_RS06585 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | garD: meso-galactarate dehydratase (L-threo-forming) GarD | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | PsAD2_RS16780 | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | PsAD2_RS03450 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | PsAD2_RS17655 | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | PsAD2_RS21775 | PsAD2_RS21770 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | PsAD2_RS16780 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | PsAD2_RS02835 | |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | PsAD2_RS02835 | PsAD2_RS08285 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | dctQ: L-malate TRAP tranpsorter, small permease component DctQ | PsAD2_RS05440 | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | PsAD2_RS09320 | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | PsAD2_RS02835 | PsAD2_RS08285 |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | PsAD2_RS11825 | PsAD2_RS19615 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | PsAD2_RS01050 | PsAD2_RS05610 |
| mannitol | mt1d: mannitol 1-dehydrogenase | | |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | STP6: mannose:H+ symporter | | |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | PsAD2_RS12360 | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | PsAD2_RS21775 | PsAD2_RS21770 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | PsAD2_RS17655 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | PsAD2_RS22715 | PsAD2_RS12315 |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | PsAD2_RS02870 | PsAD2_RS22995 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | PsAD2_RS02835 | PsAD2_RS07415 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | PsAD2_RS02810 | |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | PsAD2_RS22715 | PsAD2_RS12315 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | PsAD2_RS23255 | PsAD2_RS17200 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | PsAD2_RS08865 | PsAD2_RS20330 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | PsAD2_RS20310 | PsAD2_RS23265 |
| pyruvate | dctM: pyruvate TRAP transporter, large permease component | PsAD2_RS06000 | PsAD2_RS00685 |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | PsAD2_RS00680 | PsAD2_RS05995 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | PsAD2_RS06355 | PsAD2_RS18230 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | PsAD2_RS01750 | PsAD2_RS20325 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| sorbitol | scrK: fructokinase | PsAD2_RS05040 | PsAD2_RS21780 |
| sorbitol | sdh: sorbitol dehydrogenase | PsAD2_RS20325 | PsAD2_RS18845 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | dctQ: succinate TRAP transporter, small permease component DctQ | PsAD2_RS05440 | |
| sucrose | ams: sucrose hydrolase (invertase) | PsAD2_RS13380 | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | PsAD2_RS02810 | PsAD2_RS07425 |
| trehalose | treF: trehalase | PsAD2_RS13380 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | PsAD2_RS16670 | PsAD2_RS17745 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | PsAD2_RS02835 | PsAD2_RS08285 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | PsAD2_RS05090 | PsAD2_RS18325 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | PsAD2_RS17560 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | PsAD2_RS17880 | |
| xylose | DKDP-dehydrog: D-2-keto-3-deoxypentoate dehydrogenase | PsAD2_RS05655 | PsAD2_RS20325 |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | PsAD2_RS21535 | PsAD2_RS14045 |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | PsAD2_RS21540 | PsAD2_RS14040 |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | PsAD2_RS21545 | PsAD2_RS14035 |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | PsAD2_RS21550 | PsAD2_RS14030 |
| xylose | HDOP-hydrol: 5-hydroxy-2,4-dioxopentanonate hydrolase | PsAD2_RS22500 | |
| xylose | xad: D-xylonate dehydratase | PsAD2_RS04990 | |
| xylose | xdh: D-xylose dehydrogenase | PsAD2_RS05695 | PsAD2_RS00800 |
| xylose | xylC: xylonolactonase | PsAD2_RS03450 | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 24 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:
- 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