Potential Gaps in catabolism of small carbon sources in Sedimenticola selenatireducens DSM 17993
Found 110 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
acetate | actP: cation/acetate symporter ActP | | |
alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | A3GO_RS0114190 | A3GO_RS0114160 |
alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | A3GO_RS0114215 | A3GO_RS0114165 |
alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | A3GO_RS0114175 | A3GO_RS0114425 |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) | A3GO_RS0106830 | A3GO_RS0106835 |
arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | A3GO_RS0106845 | A3GO_RS0104265 |
arginine | rocF: arginase | A3GO_RS24575 | |
asparagine | ans: asparaginase | | |
cellobiose | cbp: cellobiose phosphorylase | | |
cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | A3GO_RS0106845 | A3GO_RS0104265 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | A3GO_RS0106830 | A3GO_RS0106835 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | A3GO_RS0106835 | A3GO_RS0106830 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | A3GO_RS0106840 | |
citrulline | arcC: carbamate kinase | | |
D-alanine | AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 | A3GO_RS0114175 | A3GO_RS0114425 |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | A3GO_RS0118715 | A3GO_RS0117900 |
deoxyinosine | deoB: phosphopentomutase | A3GO_RS26720 | A3GO_RS24860 |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | A3GO_RS0105425 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | A3GO_RS0115810 | |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | garK: glycerate 2-kinase | A3GO_RS0117290 | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
fructose | Slc2a5: fructose:H+ symporter | | |
fucose | aldA: lactaldehyde dehydrogenase | A3GO_RS0115130 | A3GO_RS0114560 |
fucose | fucA: L-fuculose-phosphate aldolase FucA | A3GO_RS0121690 | |
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 | 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 | A3GO_RS0115130 | A3GO_RS0114560 |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | gci: D-galactarolactone cycloisomerase | | |
galacturonate | gli: D-galactarolactone isomerase | | |
galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | A3GO_RS0102965 | |
galacturonate | udh: D-galacturonate dehydrogenase | | |
gluconate | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
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) | A3GO_RS0103505 | |
glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | garK: glycerate 2-kinase | A3GO_RS0117290 | |
glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | A3GO_RS0102965 | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | A3GO_RS0114215 | A3GO_RS0114165 |
glutamate | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | A3GO_RS0114210 | A3GO_RS0114170 |
glutamate | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | A3GO_RS0114175 | A3GO_RS0114425 |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | A3GO_RS0114215 | A3GO_RS0114165 |
histidine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | A3GO_RS0114210 | A3GO_RS0114170 |
histidine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | A3GO_RS0114175 | A3GO_RS0114425 |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | A3GO_RS0109385 | A3GO_RS0118285 |
isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | A3GO_RS0114215 | A3GO_RS0114165 |
L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
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) | A3GO_RS0114215 | A3GO_RS0114165 |
lysine | davA: 5-aminovaleramidase | A3GO_RS0113290 | A3GO_RS0105545 |
lysine | davB: L-lysine 2-monooxygenase | | |
lysine | davT: 5-aminovalerate aminotransferase | A3GO_RS0110380 | A3GO_RS0109800 |
lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | A3GO_RS0108695 | A3GO_RS0114400 |
lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | A3GO_RS0106830 | A3GO_RS0106835 |
lysine | hisP: L-lysine ABC transporter, ATPase component HisP | A3GO_RS0106845 | A3GO_RS0104265 |
lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | A3GO_RS0106835 | A3GO_RS0106830 |
maltose | malA: 6-phospho-alphaglucosidase | | |
maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
mannitol | mt2d: mannitol 2-dehydrogenase | A3GO_RS0109385 | A3GO_RS0118285 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | manA: mannose-6-phosphate isomerase | A3GO_RS0108450 | A3GO_RS26720 |
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 | A3GO_RS0113465 | A3GO_RS0110470 |
myoinositol | iolT: myo-inositol:H+ symporter | | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | A3GO_RS0103505 | |
NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | A3GO_RS0114215 | A3GO_RS0114165 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | A3GO_RS0114190 | A3GO_RS0114160 |
propionate | putP: propionate transporter; proline:Na+ symporter | | |
putrescine | gabT: gamma-aminobutyrate transaminase | A3GO_RS0108935 | A3GO_RS0110520 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | A3GO_RS0110380 | A3GO_RS0108935 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | A3GO_RS0117140 | A3GO_RS0115130 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
rhamnose | aldA: lactaldehyde dehydrogenase | A3GO_RS0115130 | A3GO_RS0114560 |
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 | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | A3GO_RS0114190 | A3GO_RS0114160 |
serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | A3GO_RS0114215 | A3GO_RS0114165 |
serine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | A3GO_RS0114175 | A3GO_RS0114425 |
sorbitol | sdh: sorbitol dehydrogenase | A3GO_RS0104110 | A3GO_RS0118285 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | SUS: sucrose synthase | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | A3GO_RS0114190 | A3GO_RS0114160 |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | A3GO_RS0114215 | A3GO_RS0114165 |
threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | A3GO_RS0114175 | A3GO_RS0114425 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | A3GO_RS0118780 | A3GO_RS24555 |
threonine | ltaE: L-threonine aldolase | A3GO_RS0100345 | |
thymidine | deoA: thymidine phosphorylase DeoA | A3GO_RS0110755 | |
thymidine | deoB: phosphopentomutase | A3GO_RS26720 | A3GO_RS24860 |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | PsTP: trehalose phosphorylase | | |
trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | A3GO_RS0114180 | A3GO_RS0114200 |
tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | A3GO_RS0114170 | A3GO_RS0114210 |
tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | A3GO_RS0114165 | A3GO_RS0114215 |
tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | A3GO_RS0114190 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | A3GO_RS0114405 | A3GO_RS0108710 |
valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | A3GO_RS0114215 | A3GO_RS0114165 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | A3GO_RS23760 | A3GO_RS0115125 |
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