Potential Gaps in catabolism of small carbon sources in Phaeobacter inhibens BS107
Found 53 low-confidence and 46 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | PGA1_c04560 | |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | PGA1_c04090 | PGA1_c34350 |
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | PGA1_c06210 | |
| 4-hydroxybenzoate | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | PGA1_c06200 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| acetate | ybhL: acetate uptake transporter YbhL | PGA1_c21920 | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | PGA1_c07370 | PGA1_c13170 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | PGA1_c11550 | PGA1_262p02380 |
| arginine | artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) | PGA1_262p02370 | PGA1_c11560 |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | PGA1_262p02360 | |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | PGA1_262p02370 | PGA1_c26600 |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | PGA1_c11550 | PGA1_262p02380 |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | PGA1_262p02350 | PGA1_c11580 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | PGA1_c01980 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | PGA1_c01990 | |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | PGA1_c02000 | PGA1_65p00120 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | PGA1_c02010 | PGA1_262p02350 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | PGA1_c33720 | PGA1_c04590 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | PGA1_c03970 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | PGA1_c03950 | PGA1_c26920 |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | PGA1_c28160 | PGA1_c03940 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | PGA1_c31360 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | PGA1_c08400 | |
| deoxyribose | deoK: deoxyribokinase | PGA1_c34980 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | PGA1_c21070 | PGA1_c32800 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | PGA1_c16250 | |
| 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 | dgoD: D-galactonate dehydratase | PGA1_c07380 | PGA1_c04540 |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | PGA1_c07360 | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garK: glycerate 2-kinase | PGA1_c31360 | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | PGA1_c31400 | PGA1_c19370 |
| glucuronate | garR: tartronate semialdehyde reductase | PGA1_c14880 | PGA1_c17360 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | PGA1_c04540 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | hutX: L-histidine ABC transporter, substrate-binding component HutX | PGA1_c25570 | PGA1_c22800 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoD: D-galactonate dehydratase | PGA1_c07380 | PGA1_c04540 |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | PGA1_c07360 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| lysine | davA: 5-aminovaleramidase | PGA1_c26450 | PGA1_c34700 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | PGA1_c24230 | PGA1_c28750 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | PGA1_c11550 | PGA1_262p02380 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | PGA1_c02010 | PGA1_262p02350 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | PGA1_262p02370 | PGA1_c26600 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | PGA1_c13210 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | PGA1_c13200 | PGA1_c16700 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | PGA1_c13190 | |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | PGA1_c13180 | PGA1_c16680 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | PGA1_c36500 | PGA1_262p01980 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | PGA1_c36500 | PGA1_262p01980 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | PGA1_c34400 | PGA1_c09350 |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | PGA1_c32250 | PGA1_c21670 |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | PGA1_c21070 | PGA1_c32800 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | PGA1_c27390 | PGA1_c13170 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | PGA1_c31400 | PGA1_c19370 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | PGA1_c34980 | |
| serine | snatA: L-serine transporter | PGA1_c19770 | |
| threonine | snatA: L-threonine transporter snatA | PGA1_c19770 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | PGA1_c10280 | PGA1_c17340 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | PGA1_c17300 | PGA1_c21670 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | PGA1_c34320 | PGA1_c13170 |
| xylose | xylF: ABC transporter for xylose, substrate binding component xylF | PGA1_262p00430 | |
| xylose | xylH: ABC transporter for xylose, permease component xylH | PGA1_262p00440 | PGA1_c28050 |
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 (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