GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Streptacidiphilus oryzae TH49

Found 48 low-confidence and 72 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaB: 3-carboxymuconate cycloisomerase
4-hydroxybenzoate pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) BS73_RS10025
4-hydroxybenzoate pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) BS73_RS10020
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK BS73_RS06270
alanine cycA: L-alanine symporter CycA BS73_RS16535 BS73_RS10785
arabinose xylHsa: L-arabinose ABC transporter, permease component XylH BS73_RS06550 BS73_RS07055
arginine adiA: arginine decarboxylase (AdiA/SpeA) BS73_RS05790
arginine aguB: N-carbamoylputrescine hydrolase BS73_RS30130 BS73_RS27285
arginine patA: putrescine aminotransferase (PatA/SpuC) BS73_RS14265 BS73_RS18925
arginine rocE: L-arginine permease BS73_RS16535 BS73_RS10785
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BS73_RS15740 BS73_RS01465
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BS73_RS15735 BS73_RS01490
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BS73_RS15735
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase BS73_RS12295 BS73_RS24175
D-alanine dadA: D-alanine dehydrogenase
D-serine cycA: D-serine:H+ symporter CycA BS73_RS10785 BS73_RS16535
D-serine dsdA: D-serine ammonia-lyase BS73_RS17825 BS73_RS16930
deoxyinosine deoB: phosphopentomutase BS73_RS23610 BS73_RS22910
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BS73_RS15485 BS73_RS09090
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter BS73_RS27515 BS73_RS31945
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme BS73_RS10685
deoxyribose deoK: deoxyribokinase BS73_RS29490 BS73_RS17345
deoxyribose deoP: deoxyribose transporter
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase BS73_RS15485 BS73_RS00110
fucose KDF-hydrolase: 2,4-diketo-3-deoxy-L-fuconate hydrolase BS73_RS30775 BS73_RS00400
galactose galE: UDP-glucose 4-epimerase BS73_RS17235 BS73_RS22190
galactose galP: galactose:H+ symporter GalP BS73_RS29790 BS73_RS21860
galacturonate PS417_04205: D-galacturonate transporter BS73_RS04730
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) BS73_RS16650 BS73_RS15815
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxuL: D-glucaro-1,5-lactonase UxuL or UxuF
glutamate yveA: L-glutamate:H+ symporter YveA BS73_RS16525 BS73_RS29095
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) BS73_RS23040 BS73_RS10545
histidine hutG': N-formylglutamate amidohydrolase
histidine PA5503: L-histidine ABC transporter, ATPase component BS73_RS08870 BS73_RS32880
histidine PA5504: L-histidine ABC transporter, permease component BS73_RS35970
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BS73_RS23635 BS73_RS25280
lactose galE: UDP-glucose 4-epimerase BS73_RS17235 BS73_RS22190
lactose lacP: lactose permease LacP
leucine liuC: 3-methylglutaconyl-CoA hydratase BS73_RS14910 BS73_RS33895
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BS73_RS25285 BS73_RS00480
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
lysine cadA: lysine decarboxylase BS73_RS13335 BS73_RS03380
lysine davD: glutarate semialdehyde dehydrogenase BS73_RS19435 BS73_RS01225
lysine gcdG: succinyl-CoA:glutarate CoA-transferase BS73_RS32920 BS73_RS15390
lysine lysP: L-lysine:H+ symporter LysP BS73_RS16535 BS73_RS10785
lysine patA: cadaverine aminotransferase BS73_RS23310 BS73_RS08925
mannitol mt2d: mannitol 2-dehydrogenase BS73_RS07840 BS73_RS11735
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE BS73_RS07825
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) BS73_RS07830 BS73_RS30605
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) BS73_RS07835 BS73_RS31740
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG BS73_RS18100 BS73_RS14235
mannose manP: mannose PTS system, EII-CBA components BS73_RS28560
myoinositol iolB: 5-deoxy-D-glucuronate isomerase BS73_RS11405
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase BS73_RS11395 BS73_RS16635
myoinositol PGA1_c07300: myo-inositol ABC transport, substrate-binding component BS73_RS29370
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BS73_RS16650 BS73_RS15815
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase BS73_RS14910 BS73_RS20300
phenylacetate paaZ1: oxepin-CoA hydrolase BS73_RS05650 BS73_RS00955
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa BS73_RS13175 BS73_RS06885
phenylalanine aroP: L-phenylalanine:H+ symporter AroP BS73_RS16535 BS73_RS25710
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase BS73_RS14910 BS73_RS20300
phenylalanine paaZ1: oxepin-CoA hydrolase BS73_RS05650 BS73_RS00955
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine pad-dh: phenylacetaldehyde dehydrogenase BS73_RS27490 BS73_RS24675
proline put1: proline dehydrogenase
propionate pccA: propionyl-CoA carboxylase, alpha subunit BS73_RS23635 BS73_RS25280
putrescine patA: putrescine aminotransferase (PatA/SpuC) BS73_RS14265 BS73_RS18925
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) BS73_RS14230
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) BS73_RS14225
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) BS73_RS14240
rhamnose rhaM: L-rhamnose mutarotase BS73_RS29745
ribose rbsA: D-ribose ABC transporter, ATPase component RbsA BS73_RS32735 BS73_RS01755
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB BS73_RS01760 BS73_RS13050
ribose rbsC: D-ribose ABC transporter, permease component RbsC BS73_RS01760 BS73_RS13065
ribose rbsK: ribokinase BS73_RS29490 BS73_RS17345
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BS73_RS29125 BS73_RS13625
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BS73_RS29120 BS73_RS13630
sorbitol mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK BS73_RS18100 BS73_RS14235
sorbitol sdh: sorbitol dehydrogenase BS73_RS09090 BS73_RS31130
sucrose ams: sucrose hydrolase (invertase) BS73_RS31275 BS73_RS04620
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BS73_RS29125 BS73_RS13625
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BS73_RS29120 BS73_RS13630
threonine pccA: propionyl-CoA carboxylase, alpha subunit BS73_RS23635 BS73_RS25280
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase BS73_RS23610 BS73_RS22910
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase BS73_RS04465 BS73_RS04620
tryptophan andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa BS73_RS21365 BS73_RS33040
tryptophan andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb BS73_RS12335 BS73_RS21365
tryptophan andAc: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
tryptophan andAd: athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
tryptophan mhpD: 2-hydroxypentadienoate hydratase BS73_RS04080 BS73_RS37045
tryptophan mhpE: 4-hydroxy-2-oxovalerate aldolase BS73_RS11375
tryptophan praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase BS73_RS01225 BS73_RS23595
tryptophan praC: 2-hydroxymuconate tautomerase BS73_RS17890 BS73_RS04070
tryptophan praD: 2-oxohex-3-enedioate decarboxylase BS73_RS04080 BS73_RS37045
tyrosine aroP: L-tyrosine transporter (AroP/FywP) BS73_RS16535 BS73_RS25710
tyrosine maiA: maleylacetoacetate isomerase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BS73_RS20300 BS73_RS14910
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) BS73_RS29125 BS73_RS13625
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) BS73_RS29120 BS73_RS13630
valine mmsA: methylmalonate-semialdehyde dehydrogenase BS73_RS14210 BS73_RS27490
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BS73_RS29620 BS73_RS32725
valine pccA: propionyl-CoA carboxylase, alpha subunit BS73_RS23635 BS73_RS25280
xylitol PLT5: xylitol:H+ symporter PLT5 BS73_RS21865 BS73_RS21860
xylose xylT: D-xylose transporter BS73_RS29790 BS73_RS01090

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:

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