Potential Gaps in catabolism of small carbon sources in Rhodospirillum centenum SW SW; ATCC 51521
Found 97 low-confidence and 70 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | RC1_RS17665 | RC1_RS09455 |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | RC1_RS14925 | |
alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | RC1_RS04995 | RC1_RS05000 |
alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | RC1_RS08780 | |
alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | RC1_RS08790 | RC1_RS08795 |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | RC1_RS14990 | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | RC1_RS08780 | |
arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | RC1_RS08785 | |
arginine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | RC1_RS08790 | RC1_RS12190 |
asparagine | bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB) | RC1_RS14935 | |
asparagine | bztC: aspartate/asparagine ABC transporter, permease component 2 (BztC) | RC1_RS14940 | |
asparagine | bztD: aspartate/asparagine ABC transporter, ATPase component (BztD) | RC1_RS14945 | RC1_RS14340 |
aspartate | bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB) | RC1_RS14935 | |
aspartate | bztC: aspartate/asparagine ABC transporter, permease component 2 (BztC) | RC1_RS14940 | |
aspartate | bztD: aspartate/asparagine ABC transporter, ATPase component (BztD) | RC1_RS14945 | RC1_RS14340 |
cellobiose | bgl: cellobiase | | |
cellobiose | SemiSWEET: Sugar transporter SemiSWEET | RC1_RS12330 | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | RC1_RS14340 | RC1_RS14945 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | RC1_RS12980 | RC1_RS12975 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | RC1_RS12975 | RC1_RS12980 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | RC1_RS12965 | |
citrulline | citrullinase: putative citrullinase | RC1_RS03115 | |
D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | RC1_RS08785 | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | RC1_RS15805 | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | RC1_RS03695 | RC1_RS15150 |
deoxyinosine | deoB: phosphopentomutase | RC1_RS08135 | RC1_RS08600 |
deoxyinosine | deoD: deoxyinosine phosphorylase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | RC1_RS07525 | RC1_RS18990 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | RC1_RS16890 | |
deoxyribose | deoP: deoxyribose transporter | | |
ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | RC1_RS07605 | RC1_RS16075 |
fructose | Slc2a5: fructose:H+ symporter | | |
fucose | aldA: lactaldehyde dehydrogenase | RC1_RS06940 | RC1_RS07630 |
fucose | fucA: L-fuculose-phosphate aldolase FucA | RC1_RS14990 | |
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 | | |
fumarate | dctA: fumarate:H+ symporter DctA | | |
galactose | galE: UDP-glucose 4-epimerase | RC1_RS12210 | RC1_RS22390 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | RC1_RS07630 | RC1_RS18020 |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | gci: D-galactarolactone cycloisomerase | | |
galacturonate | gli: D-galactarolactone isomerase | | |
galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | RC1_RS07200 | |
galacturonate | udh: D-galacturonate dehydrogenase | | |
gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
gluconate | gntK: D-gluconate kinase | | |
gluconate | gntT: gluconate:H+ symporter GntT | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | RC1_RS16035 | |
glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
glucose | SemiSWEET: Sugar transporter SemiSWEET | RC1_RS12330 | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | RC1_RS07630 | RC1_RS18020 |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | RC1_RS07200 | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | RC1_RS08780 | |
glutamate | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | RC1_RS08785 | |
glutamate | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | RC1_RS08790 | RC1_RS12190 |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | RC1_RS01225 | |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | PA5503: L-histidine ABC transporter, ATPase component | RC1_RS16055 | RC1_RS14945 |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | RC1_RS06450 | RC1_RS01895 |
isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | RC1_RS08780 | |
L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | RC1_RS15405 | |
L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
lactose | galE: UDP-glucose 4-epimerase | RC1_RS12210 | RC1_RS22390 |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | RC1_RS08780 | |
lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | RC1_RS12965 | RC1_RS12970 |
lysine | davA: 5-aminovaleramidase | RC1_RS03115 | |
lysine | davB: L-lysine 2-monooxygenase | | |
lysine | davT: 5-aminovalerate aminotransferase | RC1_RS02625 | RC1_RS11870 |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | RC1_RS07275 | RC1_RS15585 |
lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | RC1_RS12980 | RC1_RS12975 |
lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | RC1_RS12975 | RC1_RS12980 |
maltose | susB: alpha-glucosidase (maltase) | RC1_RS08160 | RC1_RS15920 |
maltose | thuK: maltose ABC transporter, ATPase component ThuK | RC1_RS17855 | RC1_RS06975 |
mannitol | manA: mannose-6-phosphate isomerase | RC1_RS00780 | |
mannitol | mt1d: mannitol 1-dehydrogenase | RC1_RS16075 | |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | manA: mannose-6-phosphate isomerase | RC1_RS00780 | |
mannose | STP6: mannose:H+ symporter | | |
myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | RC1_RS19465 | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | RC1_RS07630 | RC1_RS06940 |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | RC1_RS16035 | |
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 | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | RC1_RS12905 | RC1_RS03020 |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | RC1_RS18865 | RC1_RS09350 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | RC1_RS18865 | RC1_RS09350 |
phenylacetate | paaK: phenylacetate-CoA ligase | RC1_RS17570 | RC1_RS16880 |
phenylacetate | paaZ1: oxepin-CoA hydrolase | RC1_RS12905 | RC1_RS14595 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylacetate | ppa: phenylacetate permease ppa | RC1_RS12730 | |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | RC1_RS08780 | |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | RC1_RS05000 | RC1_RS04995 |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
proline | AZOBR_RS08240: proline ABC transporter, permease component 2 | RC1_RS08785 | |
propionate | lctP: propionate permease | RC1_RS15805 | |
putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | RC1_RS06980 | |
rhamnose | aldA: lactaldehyde dehydrogenase | RC1_RS06940 | RC1_RS07630 |
rhamnose | rhaA: L-rhamnose isomerase | | |
rhamnose | rhaB: L-rhamnulokinase | | |
rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
rhamnose | rhaM: L-rhamnose mutarotase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | RC1_RS04995 | RC1_RS05000 |
serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | RC1_RS08780 | |
serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | RC1_RS08790 | RC1_RS08795 |
sorbitol | sdh: sorbitol dehydrogenase | RC1_RS18590 | RC1_RS07525 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
succinate | sdc: succinate:Na+ symporter Sdc | | |
sucrose | ams: sucrose hydrolase (invertase) | RC1_RS08160 | RC1_RS15920 |
sucrose | thuK: sucrose ABC transporter, ATPase component ThuK | RC1_RS17855 | RC1_RS06975 |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | RC1_RS04995 | RC1_RS05000 |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | RC1_RS08780 | |
threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | RC1_RS08790 | RC1_RS08795 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | RC1_RS17505 | RC1_RS17500 |
threonine | ltaE: L-threonine aldolase | RC1_RS08280 | RC1_RS06420 |
thymidine | deoB: phosphopentomutase | RC1_RS08135 | RC1_RS08600 |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | thuK: trehalose ABC transporter, ATPase component ThuK | RC1_RS17855 | RC1_RS06975 |
trehalose | treF: trehalase | RC1_RS08160 | RC1_RS15920 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
valine | acdH: isobutyryl-CoA dehydrogenase | RC1_RS06450 | RC1_RS01895 |
valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | RC1_RS08780 | |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | RC1_RS18020 | RC1_RS07630 |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
xylose | xylA: xylose isomerase | | |
xylose | xylB: xylulokinase | | |
xylose | xylT: D-xylose transporter | | |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Apr 09 2024. 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