GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Nitriliruptor alkaliphilus DSM 45188

Found 66 low-confidence and 86 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 pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase NITAL_RS23530 NITAL_RS08565
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
acetate actP: cation/acetate symporter ActP NITAL_RS20995
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) NITAL_RS00050
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) NITAL_RS00060 NITAL_RS01160
arabinose gguA: L-arabinose ABC transporter, ATPase component GguA NITAL_RS04930 NITAL_RS15475
arginine arcA: arginine deiminase NITAL_RS26115
arginine put1: proline dehydrogenase NITAL_RS10705 NITAL_RS21835
arginine putA: L-glutamate 5-semialdeyde dehydrogenase NITAL_RS10705 NITAL_RS05175
arginine rocE: L-arginine permease
asparagine ans: asparaginase NITAL_RS07045 NITAL_RS02525
asparagine dauA: dicarboxylic acid transporter DauA NITAL_RS15805
aspartate dauA: dicarboxylic acid transporter DauA NITAL_RS15805
cellobiose glk: glucokinase NITAL_RS20430 NITAL_RS15465
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC NITAL_RS23935
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component NITAL_RS18660 NITAL_RS08255
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 NITAL_RS09965 NITAL_RS08245
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline put1: proline dehydrogenase NITAL_RS10705 NITAL_RS21835
citrulline putA: L-glutamate 5-semialdeyde dehydrogenase NITAL_RS10705 NITAL_RS05175
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase NITAL_RS02880 NITAL_RS01010
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component NITAL_RS17600 NITAL_RS18225
deoxyinosine deoB: phosphopentomutase NITAL_RS14955 NITAL_RS01650
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 NITAL_RS17590
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 NITAL_RS05680 NITAL_RS17585
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase NITAL_RS01710 NITAL_RS12765
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fucose fucD: L-fuconate dehydratase NITAL_RS01720
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase NITAL_RS05180 NITAL_RS03800
fucose fucP: L-fucose:H+ symporter FucP
galactose galK: galactokinase (-1-phosphate forming) NITAL_RS08120
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase NITAL_RS08090
galactose gguA: galactose ABC transporter, ATPase component GguA NITAL_RS04930 NITAL_RS15475
galactose pgmA: alpha-phosphoglucomutase NITAL_RS10325 NITAL_RS14955
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase NITAL_RS01720
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase NITAL_RS20910
galacturonate udh: D-galacturonate dehydrogenase
gluconate edd: phosphogluconate dehydratase NITAL_RS20450
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) NITAL_RS18160 NITAL_RS14735
glucosamine nagK: N-acetylglucosamine kinase NITAL_RS19165 NITAL_RS20430
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucosamine SMc02869: N-acetylglucosamine ABC transporter, ATPase component NITAL_RS08025 NITAL_RS10750
glucose glk: glucokinase NITAL_RS20430 NITAL_RS15465
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuB: D-mannonate dehydrogenase NITAL_RS14775
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) NITAL_RS20850
glycerol glpF: glycerol facilitator glpF NITAL_RS25000
histidine hutG: N-formiminoglutamate formiminohydrolase NITAL_RS00370 NITAL_RS10775
histidine natB: L-histidine ABC transporter, substrate-binding component NatB NITAL_RS00050
histidine natC: L-histidine ABC transporter, permease component 1 (NatC) NITAL_RS00060
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component NITAL_RS11450 NITAL_RS19475
isoleucine natB: L-isoleucine ABC transporter, substrate-binding component NatB
isoleucine natC: L-isoleucine ABC transporter, permease component 1 (NatC) NITAL_RS00060 NITAL_RS06635
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit NITAL_RS10130 NITAL_RS15990
L-lactate Shew_2732: L-lactate:Na+ symporter, small component NITAL_RS21000
lactose galK: galactokinase (-1-phosphate forming) NITAL_RS08120
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase NITAL_RS08090
lactose glk: glucokinase NITAL_RS20430 NITAL_RS15465
lactose lacP: lactose permease LacP
lactose pgmA: alpha-phosphoglucomutase NITAL_RS10325 NITAL_RS14955
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component NITAL_RS11450 NITAL_RS19475
leucine liuC: 3-methylglutaconyl-CoA hydratase NITAL_RS09215 NITAL_RS12715
leucine natB: L-leucine ABC transporter, substrate-binding component NatB NITAL_RS00050
leucine natC: L-leucine ABC transporter, permease component 1 (NatC) NITAL_RS00060 NITAL_RS06635
lysine cadA: lysine decarboxylase NITAL_RS07615 NITAL_RS22325
lysine gcdG: succinyl-CoA:glutarate CoA-transferase NITAL_RS23010 NITAL_RS00030
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase NITAL_RS04820 NITAL_RS16995
maltose glk: glucokinase NITAL_RS20430 NITAL_RS15465
mannitol mt2d: mannitol 2-dehydrogenase NITAL_RS14775 NITAL_RS24290
mannitol PLT5: polyol transporter PLT5
mannose mannokinase: D-mannose kinase NITAL_RS19165 NITAL_RS20430
mannose TM1746: mannose ABC transporter, substrate-binding component NITAL_RS14700
mannose TM1750: mannose ABC transporter, ATPase component 2 NITAL_RS18330 NITAL_RS04355
myoinositol iolB: 5-deoxy-D-glucuronate isomerase NITAL_RS09025
myoinositol iolE: scyllo-inosose 2-dehydratase NITAL_RS09050
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase NITAL_RS09015
myoinositol PGA1_c07300: myo-inositol ABC transport, substrate-binding component NITAL_RS09055
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) NITAL_RS18160 NITAL_RS14735
NAG nagK: N-acetylglucosamine kinase NITAL_RS19165 NITAL_RS20430
NAG SMc02869: N-acetylglucosamine ABC transporter, ATPase component NITAL_RS08025 NITAL_RS10750
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
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase NITAL_RS10870 NITAL_RS09215
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase NITAL_RS23530 NITAL_RS08565
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase NITAL_RS23530 NITAL_RS08565
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase NITAL_RS24425 NITAL_RS08560
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) NITAL_RS08770 NITAL_RS01165
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
phenylalanine livM: L-phenylalanine ABC transporter, permease component 2 (LivM) NITAL_RS01160 NITAL_RS08775
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase NITAL_RS10705 NITAL_RS21835
proline putA: L-glutamate 5-semialdeyde dehydrogenase NITAL_RS10705 NITAL_RS05175
propionate pccA: propionyl-CoA carboxylase, alpha subunit NITAL_RS10130 NITAL_RS15990
propionate putP: propionate transporter; proline:Na+ symporter NITAL_RS02495
putrescine gabT: gamma-aminobutyrate transaminase NITAL_RS08275 NITAL_RS06900
putrescine patA: putrescine aminotransferase (PatA/SpuC) NITAL_RS06900 NITAL_RS10730
putrescine potA: putrescine ABC transporter, ATPase component (PotA/PotG) NITAL_RS10750 NITAL_RS16185
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) NITAL_RS10765
pyruvate actP: large subunit of pyruvate transporter (actP-like) NITAL_RS20995
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) NITAL_RS21000
rhamnose LRA1: L-rhamnofuranose dehydrogenase NITAL_RS12765 NITAL_RS12625
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase NITAL_RS22550 NITAL_RS11395
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) NITAL_RS00050
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) NITAL_RS00060 NITAL_RS01160
sorbitol sdh: sorbitol dehydrogenase NITAL_RS02620 NITAL_RS24290
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase) NITAL_RS20655 NITAL_RS18165
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) NITAL_RS00050
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) NITAL_RS00060 NITAL_RS01160
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) NITAL_RS19465 NITAL_RS09120
thymidine deoB: phosphopentomutase NITAL_RS14955 NITAL_RS01650
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase NITAL_RS20430 NITAL_RS15465
trehalose treF: trehalase NITAL_RS18165 NITAL_RS08015
tryptophan tnaA: tryptophanase
tryptophan tnaT: tryptophan:Na+ symporter TnaT NITAL_RS18040
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase NITAL_RS12795 NITAL_RS20410
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component NITAL_RS11450 NITAL_RS19475
valine mmsA: methylmalonate-semialdehyde dehydrogenase NITAL_RS09035 NITAL_RS22635
valine mmsB: 3-hydroxyisobutyrate dehydrogenase NITAL_RS06180
valine natB: L-valine ABC transporter, substrate-binding component NatB
valine natC: L-valine ABC transporter, permease component 1 (NatC) NITAL_RS00060 NITAL_RS06635
valine pccA: propionyl-CoA carboxylase, alpha subunit NITAL_RS10130 NITAL_RS15990
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase NITAL_RS19730 NITAL_RS07465
xylose xylG: ABC transporter for xylose, ATP-binding component xylG NITAL_RS04930 NITAL_RS15475

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