Potential Gaps in catabolism of small carbon sources in Skermanella stibiiresistens SB22
Found 37 low-confidence and 76 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | N825_RS19860 | N825_RS07775 |
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | N825_RS01845 | N825_RS12900 |
| 4-hydroxybenzoate | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | N825_RS01850 | N825_RS12895 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | N825_RS34130 | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | N825_RS03725 | N825_RS03285 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | N825_RS03260 | N825_RS16515 |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | N825_RS03275 | N825_RS15205 |
| arabinose | xacC: L-arabinono-1,4-lactonase | N825_RS25455 | N825_RS02215 |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | N825_RS03260 | N825_RS16515 |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | N825_RS03265 | N825_RS05145 |
| asparagine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | N825_RS06455 | N825_RS04005 |
| asparagine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | N825_RS06450 | N825_RS33165 |
| asparagine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | N825_RS06460 | N825_RS14310 |
| aspartate | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | N825_RS06455 | N825_RS04005 |
| aspartate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | N825_RS06450 | N825_RS33165 |
| aspartate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | N825_RS06460 | N825_RS14310 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | N825_RS00145 | N825_RS06450 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | N825_RS00130 | N825_RS14310 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | N825_RS00135 | N825_RS04005 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | N825_RS02255 | N825_RS00140 |
| citrulline | citrullinase: putative citrullinase | N825_RS19545 | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | N825_RS19980 | N825_RS12530 |
| deoxyinosine | deoB: phosphopentomutase | N825_RS16950 | N825_RS20170 |
| deoxyinosine | H281DRAFT_01112: deoxynucleoside transporter, permease component 2 | N825_RS18950 | N825_RS10415 |
| deoxyinosine | H281DRAFT_01113: deoxynucleoside transporter, ATPase component | N825_RS18955 | N825_RS06180 |
| deoxyinosine | H281DRAFT_01114: deoxynucleoside transporter, substrate-binding component | N825_RS18960 | N825_RS01530 |
| deoxyinosine | H281DRAFT_01115: deoxynucleoside transporter, permease component 1 | N825_RS18945 | N825_RS01515 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | N825_RS13450 | N825_RS17750 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | N825_RS13450 | N825_RS17750 |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | N825_RS18835 | N825_RS17715 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | N825_RS12455 | |
| fucose | HSERO_RS05255: ABC transporter for L-fucose, permease component | N825_RS13095 | N825_RS05320 |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | N825_RS03560 | |
| galactose | dgoD: D-galactonate dehydratase | N825_RS21145 | N825_RS10340 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | garD: meso-galactarate dehydratase (L-threo-forming) GarD | N825_RS29945 | N825_RS16600 |
| gluconate | gntK: D-gluconate kinase | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | N825_RS29855 | |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glucuronate | gudD: D-glucarate dehydratase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | N825_RS20570 | |
| histidine | Ac3H11_2555: L-histidine ABC transporter, substrate-binding component 2 | N825_RS04010 | |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | N825_RS03260 | N825_RS16515 |
| lactose | dgoD: D-galactonate dehydratase | N825_RS21145 | N825_RS10340 |
| lactose | lacP: lactose permease LacP | | |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | N825_RS03260 | N825_RS16515 |
| lysine | davA: 5-aminovaleramidase | N825_RS04475 | N825_RS19545 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | N825_RS22125 | N825_RS18655 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | N825_RS02640 | N825_RS10970 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| maltose | susB: alpha-glucosidase (maltase) | N825_RS17020 | N825_RS33845 |
| mannitol | mt2d: mannitol 2-dehydrogenase | N825_RS28205 | N825_RS19190 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | N825_RS19210 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | N825_RS19205 | N825_RS06690 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | N825_RS06700 | N825_RS19195 |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | N825_RS18425 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | N825_RS29855 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| phenylacetate | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylacetate | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | N825_RS19860 | N825_RS07775 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | N825_RS19860 | N825_RS07775 |
| phenylacetate | paaK: phenylacetate-CoA ligase | N825_RS26760 | N825_RS10580 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | N825_RS33380 | N825_RS27875 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | N825_RS04400 | N825_RS22230 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | N825_RS03260 | N825_RS16515 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | N825_RS03725 | N825_RS03285 |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | N825_RS14715 | N825_RS03170 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | N825_RS08990 | |
| putrescine | puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase | N825_RS32720 | N825_RS20855 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | N825_RS21525 | N825_RS31950 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | N825_RS05325 | N825_RS13090 |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | N825_RS05320 | N825_RS13095 |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | N825_RS03725 | N825_RS03285 |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | N825_RS03260 | N825_RS16515 |
| serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | N825_RS03275 | N825_RS15205 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | N825_RS06700 | N825_RS19195 |
| sorbitol | sdh: sorbitol dehydrogenase | N825_RS01350 | N825_RS19190 |
| sucrose | ams: sucrose hydrolase (invertase) | N825_RS33845 | N825_RS17020 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | N825_RS03725 | N825_RS03285 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | N825_RS03260 | N825_RS16515 |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | N825_RS03275 | N825_RS15205 |
| thymidine | deoB: phosphopentomutase | N825_RS16950 | N825_RS20170 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | N825_RS17020 | N825_RS33845 |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | N825_RS34110 | |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | N825_RS34115 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | N825_RS34120 | N825_RS26365 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | kyn: kynureninase | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
| tryptophan | kynB: kynurenine formamidase | N825_RS30770 | N825_RS29830 |
| tryptophan | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | N825_RS19860 | N825_RS07775 |
| tryptophan | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | N825_RS01845 | N825_RS12900 |
| tryptophan | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | N825_RS01850 | N825_RS12895 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | N825_RS03260 | N825_RS16515 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | N825_RS35530 | N825_RS01910 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | N825_RS18055 | N825_RS18730 |
| xylitol | Dshi_0546: xylitol ABC transporter, ATPase component | N825_RS19140 | N825_RS06700 |
| xylitol | xdhA: xylitol dehydrogenase | N825_RS19135 | N825_RS28175 |
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