GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Algoriphagus machipongonensis PR1

Found 86 low-confidence and 48 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
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
acetate actP: cation/acetate symporter ActP ALPR1_RS02865
arabinose Echvi_1880: L-arabinose:Na+ symporter ALPR1_RS12485 ALPR1_RS16525
arabinose xacB: L-arabinose 1-dehydrogenase ALPR1_RS16160 ALPR1_RS17925
arabinose xacC: L-arabinono-1,4-lactonase ALPR1_RS03685
arginine rocE: L-arginine permease
arginine rocF: arginase ALPR1_RS12720
cellobiose bgl: cellobiase
cellobiose glk: glucokinase ALPR1_RS14545 ALPR1_RS05845
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component ALPR1_RS09775 ALPR1_RS13410
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate larD: D,L-lactic acid transporter ALPR1_RS19200
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase ALPR1_RS03120
deoxyinosine deoB: phosphopentomutase ALPR1_RS10665
deoxyinosine nupC: deoxyinosine:H+ symporter NupC ALPR1_RS10400
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase ALPR1_RS17925 ALPR1_RS12235
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase ALPR1_RS10625
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter ALPR1_RS13860
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) ALPR1_RS01365 ALPR1_RS12235
fucose fucD: L-fuconate dehydratase ALPR1_RS11090
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase ALPR1_RS13840 ALPR1_RS17925
fucose fuconolactonase: L-fucono-1,5-lactonase ALPR1_RS13850
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) ALPR1_RS05850 ALPR1_RS20085
glucose glk: glucokinase ALPR1_RS14545 ALPR1_RS05845
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctP: D-glucuronate TRAP transporter, solute receptor component ALPR1_RS17480
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent ALPR1_RS03870
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) ALPR1_RS19190
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase ALPR1_RS02465 ALPR1_RS19205
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit ALPR1_RS18330 ALPR1_RS02675
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component ALPR1_RS14510 ALPR1_RS12815
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase ALPR1_RS16285 ALPR1_RS01095
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase ALPR1_RS17925 ALPR1_RS16160
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit ALPR1_RS12520 ALPR1_RS12915
L-lactate Shew_2732: L-lactate:Na+ symporter, small component ALPR1_RS02870
lactose glk: glucokinase ALPR1_RS14545 ALPR1_RS05845
lactose klh: periplasmic 3'-ketolactose hydrolase ALPR1_RS07255 ALPR1_RS15135
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) ALPR1_RS18010 ALPR1_RS11665
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit ALPR1_RS17980 ALPR1_RS18960
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit ALPR1_RS18330 ALPR1_RS02675
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component ALPR1_RS14510 ALPR1_RS12815
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase ALPR1_RS19205 ALPR1_RS02465
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ALPR1_RS12520 ALPR1_RS12915
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit ALPR1_RS14955 ALPR1_RS04635
lysine cadA: lysine decarboxylase ALPR1_RS02910
lysine davD: glutarate semialdehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06445
lysine davT: 5-aminovalerate aminotransferase ALPR1_RS03490 ALPR1_RS09710
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine lysP: L-lysine:H+ symporter LysP
lysine patD: 5-aminopentanal dehydrogenase ALPR1_RS01205 ALPR1_RS06860
maltose glk: glucokinase ALPR1_RS14545 ALPR1_RS05845
maltose susB: alpha-glucosidase (maltase)
mannitol mt2d: mannitol 2-dehydrogenase ALPR1_RS17925 ALPR1_RS16160
mannitol PLT5: polyol transporter PLT5
mannose man-isomerase: D-mannose isomerase
mannose STP6: mannose:H+ symporter
myoinositol iolG: myo-inositol 2-dehydrogenase ALPR1_RS05730
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase ALPR1_RS16075 ALPR1_RS11655
myoinositol iolT: myo-inositol:H+ symporter ALPR1_RS10185 ALPR1_RS12850
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase ALPR1_RS20075
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) ALPR1_RS05850 ALPR1_RS20085
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 ALPR1_RS16785
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase ALPR1_RS16285
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase ALPR1_RS16285 ALPR1_RS05015
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase ALPR1_RS01085 ALPR1_RS13240
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase ALPR1_RS01085 ALPR1_RS13240
phenylacetate paaK: phenylacetate-CoA ligase ALPR1_RS19255
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase ALPR1_RS00415
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline ectP: proline transporter EctP ALPR1_RS00845 ALPR1_RS01370
propionate pccA: propionyl-CoA carboxylase, alpha subunit ALPR1_RS12520 ALPR1_RS12915
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase ALPR1_RS03490 ALPR1_RS09710
putrescine patD: gamma-aminobutyraldehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate actP: large subunit of pyruvate transporter (actP-like) ALPR1_RS02865
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) ALPR1_RS02870
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter ALPR1_RS14825
sorbitol sdh: sorbitol dehydrogenase ALPR1_RS16070 ALPR1_RS08420
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 ALPR1_RS12850
sucrose ams: sucrose hydrolase (invertase) ALPR1_RS10225
threonine snatA: L-threonine transporter snatA ALPR1_RS14825
thymidine deoA: thymidine phosphorylase DeoA ALPR1_RS03280
thymidine deoB: phosphopentomutase ALPR1_RS10665
trehalose glk: glucokinase ALPR1_RS14545 ALPR1_RS05845
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase ALPR1_RS02465 ALPR1_RS19205
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit ALPR1_RS18330 ALPR1_RS02675
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component ALPR1_RS14510 ALPR1_RS12815
valine mmsA: methylmalonate-semialdehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit ALPR1_RS12520 ALPR1_RS12915
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase ALPR1_RS16070 ALPR1_RS08420

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