GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Found 30 low-confidence and 33 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
alanine alsT: L-alanine symporter AlsT/DagA HTA01S_RS13520
citrulline arcC: carbamate kinase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component HTA01S_RS18560
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 HTA01S_RS18555 HTA01S_RS13650
D-alanine Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 HTA01S_RS18550 HTA01S_RS13655
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component HTA01S_RS18545 HTA01S_RS09510
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 HTA01S_RS02550 HTA01S_RS10060
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase HTA01S_RS05325 HTA01S_RS01910
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase HTA01S_RS05325 HTA01S_RS17590
galacturonate exuT: D-galacturonate transporter ExuT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) HTA01S_RS11830
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) HTA01S_RS21120
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) HTA01S_RS18550 HTA01S_RS13395
histidine aapP: L-histidine ABC transporter, ATPase component AapP HTA01S_RS18545 HTA01S_RS09510
L-lactate Shew_2731: L-lactate:Na+ symporter, large component HTA01S_RS00855
L-lactate Shew_2732: L-lactate:Na+ symporter, small component HTA01S_RS00860
lysine argT: L-lysine ABC transporter, substrate-binding component ArgT HTA01S_RS08135 HTA01S_RS07510
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) HTA01S_RS08125 HTA01S_RS07500
lysine hisP: L-lysine ABC transporter, ATPase component HisP HTA01S_RS08115 HTA01S_RS18545
mannitol mt2d: mannitol 2-dehydrogenase HTA01S_RS01905 HTA01S_RS13445
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE HTA01S_RS01885
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) HTA01S_RS01890
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) HTA01S_RS01895 HTA01S_RS21105
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG HTA01S_RS13320 HTA01S_RS01610
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) HTA01S_RS11830
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase HTA01S_RS15600
phenylacetate ppa: phenylacetate permease ppa HTA01S_RS00870
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB HTA01S_RS23185
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase HTA01S_RS15600
propionate mctC: propionate:H+ symporter HTA01S_RS00870 HTA01S_RS00855
rhamnose rhaB: L-rhamnulokinase HTA01S_RS10190
sucrose ams: sucrose hydrolase (invertase) HTA01S_RS01635
threonine snatA: L-threonine transporter snatA HTA01S_RS09085
thymidine deoA: thymidine phosphorylase DeoA HTA01S_RS06590 HTA01S_RS15415
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase HTA01S_RS01635 HTA01S_RS11685
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine hmgA: homogentisate dioxygenase
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HTA01S_RS07615
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) HTA01S_RS16515 HTA01S_RS08705
valine mmsA: methylmalonate-semialdehyde dehydrogenase HTA01S_RS06165 HTA01S_RS16360
valine mmsB: 3-hydroxyisobutyrate dehydrogenase HTA01S_RS20760 HTA01S_RS01495
xylitol PS417_12055: xylitol ABC transporter, substrate-binding component HTA01S_RS16365
xylitol PS417_12065: xylitol ABC transporter, ATPase component HTA01S_RS08955 HTA01S_RS05330
xylitol xdhA: xylitol dehydrogenase HTA01S_RS01870 HTA01S_RS13475

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