Potential Gaps in catabolism of small carbon sources in Dinoroseobacter shibae DFL-12
Found 56 low-confidence and 54 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | Dshi_1136 | |
| 4-hydroxybenzoate | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | Dshi_1134 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | Dshi_1243 | Dshi_1358 |
| arabinose | xacC: L-arabinono-1,4-lactonase | Dshi_1240 | |
| arginine | artJ: L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT | Dshi_2222 | |
| arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | Dshi_2224 | Dshi_0320 |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | Dshi_2221 | Dshi_0321 |
| arginine | artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) | Dshi_2223 | Dshi_2224 |
| asparagine | ans: asparaginase | | |
| citrulline | PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | PS417_17595: ABC transporter for L-Citrulline, permease component 1 | Dshi_2223 | Dshi_2224 |
| citrulline | PS417_17600: ABC transporter for L-Citrulline, permease component 2 | Dshi_2224 | |
| citrulline | PS417_17605: ABC transporter for L-Citrulline, ATPase component | Dshi_2221 | Dshi_0321 |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | Dshi_0318 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | Dshi_0319 | |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | Dshi_0320 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | Dshi_0321 | Dshi_2221 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | Dshi_0888 | Dshi_1439 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Dshi_2891 | Dshi_0620 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | Dshi_3475 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| 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 | Dshi_2430 | |
| galactose | dgoD: D-galactonate dehydratase | Dshi_1244 | Dshi_0129 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | Dshi_1240 | |
| galactose | SGLT1: sodium/galactose cotransporter | Dshi_3906 | Dshi_3904 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | Dshi_1268 | Dshi_2797 |
| 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 | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Dshi_1293 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | Dshi_0604 | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | Dshi_0149 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | Dshi_3841 | |
| histidine | aapJ: L-histidine ABC transporter, substrate-binding component AapJ | Dshi_0318 | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | Dshi_0320 | |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | Dshi_0321 | Dshi_2221 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | Dshi_0319 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| L-lactate | Shew_2731: L-lactate:Na+ symporter, large component | Dshi_3556 | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | Dshi_3555 | |
| lactose | dgoD: D-galactonate dehydratase | Dshi_1244 | Dshi_0129 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | Dshi_1240 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | Dshi_0318 | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | Dshi_0320 | |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | Dshi_0321 | Dshi_2221 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | Dshi_0319 | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | Dshi_2222 | |
| lysine | davA: 5-aminovaleramidase | Dshi_3506 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | Dshi_2887 | Dshi_0577 |
| lysine | davT: 5-aminovalerate aminotransferase | Dshi_1446 | Dshi_0798 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | Dshi_2224 | Dshi_0320 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | Dshi_0321 | Dshi_2221 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | Dshi_2223 | Dshi_2224 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | Dshi_0974 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | Dshi_0973 | Dshi_3143 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | Dshi_0972 | Dshi_0549 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | Dshi_0971 | Dshi_1357 |
| mannose | man-isomerase: D-mannose isomerase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Dshi_1293 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | Dshi_3370 | Dshi_1048 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | Dshi_1762 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | Dshi_3370 | Dshi_1048 |
| proline | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | Dshi_0318 | |
| proline | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | Dshi_0320 | |
| proline | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | Dshi_0321 | Dshi_2221 |
| proline | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | Dshi_0319 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | Dshi_1366 | Dshi_2042 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | Dshi_1599 | Dshi_1053 |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | Dshi_1598 | Dshi_0549 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | | |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | Dshi_1430 | Dshi_3017 |
| putrescine | puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase | Dshi_1229 | Dshi_3925 |
| serine | snatA: L-serine transporter | Dshi_1348 | |
| sorbitol | sdh: sorbitol dehydrogenase | Dshi_0551 | Dshi_0554 |
| threonine | snatA: L-threonine transporter snatA | Dshi_1348 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | Dshi_3308 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | Dshi_1750 | Dshi_1297 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | Dshi_1747 | Dshi_0577 |
| xylose | xylT: D-xylose transporter | | |
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