Potential Gaps in catabolism of small carbon sources in Xanthobacter autotrophicus Py2
Found 71 low-confidence and 62 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | XAUT_RS11425 | XAUT_RS23680 |
alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | XAUT_RS19760 | XAUT_RS07820 |
alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | XAUT_RS19735 | XAUT_RS00230 |
alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | XAUT_RS19740 | XAUT_RS20495 |
alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | XAUT_RS19750 | XAUT_RS04450 |
arabinose | araE: L-arabinose:H+ symporter | XAUT_RS04125 | XAUT_RS04135 |
arabinose | xacB: L-arabinose 1-dehydrogenase | XAUT_RS25600 | XAUT_RS24665 |
arabinose | xacC: L-arabinono-1,4-lactonase | | |
arginine | adiA: arginine decarboxylase (AdiA/SpeA) | XAUT_RS03215 | |
arginine | patD: gamma-aminobutyraldehyde dehydrogenase | XAUT_RS13710 | XAUT_RS01855 |
asparagine | ans: asparaginase | XAUT_RS07760 | XAUT_RS05835 |
asparagine | bztA: aspartate/asparagine ABC transporter, substrate-binding component BztA | XAUT_RS23020 | XAUT_RS08225 |
asparagine | bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB) | XAUT_RS23025 | |
asparagine | bztD: aspartate/asparagine ABC transporter, ATPase component (BztD) | XAUT_RS23035 | XAUT_RS12270 |
aspartate | bztA: aspartate/asparagine ABC transporter, substrate-binding component BztA | XAUT_RS23020 | XAUT_RS08225 |
aspartate | bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB) | XAUT_RS23025 | |
aspartate | bztD: aspartate/asparagine ABC transporter, ATPase component (BztD) | XAUT_RS23035 | XAUT_RS12270 |
cellobiose | bgl: cellobiase | | |
cellobiose | MFS-glucose: glucose transporter, MFS superfamily | XAUT_RS04125 | XAUT_RS04135 |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | XAUT_RS12270 | XAUT_RS10445 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | XAUT_RS10440 | XAUT_RS00880 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | arcC: carbamate kinase | | |
citrulline | rocD: ornithine aminotransferase | XAUT_RS05230 | XAUT_RS21405 |
D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | XAUT_RS19740 | XAUT_RS20530 |
D-alanine | AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component | XAUT_RS19760 | |
D-serine | dsdA: D-serine ammonia-lyase | XAUT_RS07540 | XAUT_RS20780 |
D-serine | dsdX: D-serine transporter DsdX | XAUT_RS06190 | |
deoxyinosine | deoB: phosphopentomutase | XAUT_RS12920 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | XAUT_RS05170 | XAUT_RS14735 |
deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | XAUT_RS05170 | XAUT_RS14735 |
deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | XAUT_RS14690 | XAUT_RS21310 |
deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | XAUT_RS14685 | |
deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | XAUT_RS05365 | XAUT_RS26035 |
fucose | fucD: L-fuconate dehydratase | XAUT_RS00900 | XAUT_RS08025 |
fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
fucose | fucP: L-fucose:H+ symporter FucP | | |
galactose | galE: UDP-glucose 4-epimerase | XAUT_RS19315 | XAUT_RS23700 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | XAUT_RS04125 | XAUT_RS04135 |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galactose | pgmA: alpha-phosphoglucomutase | XAUT_RS09705 | XAUT_RS12920 |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | XAUT_RS22380 | |
glucose | MFS-glucose: glucose transporter, MFS superfamily | XAUT_RS04125 | XAUT_RS04135 |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
glycerol | glpF: glycerol facilitator glpF | XAUT_RS11670 | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | XAUT_RS05050 | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | XAUT_RS13440 | XAUT_RS13240 |
lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
lactose | MFS-glucose: glucose transporter, MFS superfamily | XAUT_RS04125 | XAUT_RS04135 |
lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
lysine | cadA: lysine decarboxylase | XAUT_RS21175 | XAUT_RS10760 |
lysine | patA: cadaverine aminotransferase | XAUT_RS06110 | XAUT_RS21405 |
lysine | patD: 5-aminopentanal dehydrogenase | XAUT_RS16460 | XAUT_RS01855 |
maltose | MFS-glucose: glucose transporter, MFS superfamily | XAUT_RS04125 | XAUT_RS04135 |
maltose | susB: alpha-glucosidase (maltase) | XAUT_RS11625 | XAUT_RS16655 |
mannitol | mt2d: mannitol 2-dehydrogenase | XAUT_RS00895 | XAUT_RS13880 |
mannitol | PLT5: polyol transporter PLT5 | XAUT_RS04125 | |
mannose | mannokinase: D-mannose kinase | | |
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 | XAUT_RS09620 | |
myoinositol | iolT: myo-inositol:H+ symporter | XAUT_RS04125 | XAUT_RS04135 |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | XAUT_RS22380 | |
NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
phenylacetate | ppa: phenylacetate permease ppa | XAUT_RS12220 | XAUT_RS04965 |
phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | XAUT_RS01975 | |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | XAUT_RS19735 | XAUT_RS05260 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | XAUT_RS19760 | XAUT_RS08115 |
proline | AZOBR_RS08240: proline ABC transporter, permease component 2 | XAUT_RS19740 | XAUT_RS20530 |
proline | AZOBR_RS08260: proline ABC transporter, substrate-binding component | XAUT_RS19760 | |
propionate | lctP: propionate permease | XAUT_RS22030 | |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | XAUT_RS13710 | XAUT_RS01855 |
putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | XAUT_RS11755 | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | XAUT_RS07715 | XAUT_RS11810 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | XAUT_RS00900 | XAUT_RS08025 |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | XAUT_RS19115 | |
serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | XAUT_RS19760 | XAUT_RS07820 |
serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | XAUT_RS19735 | XAUT_RS00230 |
serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | XAUT_RS19740 | XAUT_RS20495 |
serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | XAUT_RS19750 | XAUT_RS04450 |
sorbitol | sdh: sorbitol dehydrogenase | XAUT_RS20430 | XAUT_RS05710 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | XAUT_RS04125 | XAUT_RS04135 |
sucrose | ams: sucrose hydrolase (invertase) | | |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | XAUT_RS19760 | XAUT_RS07820 |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | XAUT_RS19735 | XAUT_RS00230 |
threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | XAUT_RS19740 | XAUT_RS20495 |
threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | XAUT_RS19750 | XAUT_RS04450 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | XAUT_RS11040 | XAUT_RS11045 |
threonine | ltaE: L-threonine aldolase | XAUT_RS21645 | XAUT_RS04355 |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | XAUT_RS12920 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | MFS-glucose: glucose transporter, MFS superfamily | XAUT_RS04125 | XAUT_RS04135 |
trehalose | treF: trehalase | | |
tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | XAUT_RS05690 | |
tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | XAUT_RS05695 | |
tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | XAUT_RS05700 | XAUT_RS05285 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | kyn: kynureninase | | |
tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
tryptophan | kynB: kynurenine formamidase | XAUT_RS03260 | |
tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | XAUT_RS19750 | XAUT_RS04450 |
tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | XAUT_RS19740 | XAUT_RS20530 |
tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | XAUT_RS19735 | XAUT_RS05260 |
tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | XAUT_RS19760 | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | XAUT_RS16330 | XAUT_RS11020 |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | XAUT_RS12245 | |
xylose | HDOP-hydrol: 5-hydroxy-2,4-dioxopentanonate hydrolase | XAUT_RS04735 | XAUT_RS20760 |
xylose | xdh: D-xylose dehydrogenase | XAUT_RS05710 | XAUT_RS25725 |
xylose | xylC: xylonolactonase | | |
xylose | xylT: D-xylose transporter | XAUT_RS04125 | XAUT_RS04135 |
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