GapMind for catabolism of small carbon sources

 

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:

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:

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:

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