GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Photobacterium jeanii R-40508

Best path

hutV, hutW, hutX, hutH, hutU, hutI, hutG

Rules

Overview: Histidine utilization in GapMind is based on MetaCyc pathways L-histidine degradation I (link) or II (link). These pathways are very similar. Other pathways in MetaCyc (III-VI) are not complete or are not reported in prokaryotes, so they are not included.

48 steps (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hutV L-histidine ABC transporter, ATPase component HutV A3K86_RS17790 A3K86_RS04635
hutW L-histidine ABC transporter, permease component HutW A3K86_RS17795
hutX L-histidine ABC transporter, substrate-binding component HutX A3K86_RS17800
hutH histidine ammonia-lyase A3K86_RS04165 A3K86_RS18720
hutU urocanase A3K86_RS04160
hutI imidazole-5-propionate hydrolase A3K86_RS04150
hutG N-formiminoglutamate formiminohydrolase A3K86_RS04155
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ A3K86_RS01705
aapM L-histidine ABC transporter, permease component 2 (AapM) A3K86_RS01695 A3K86_RS21185
aapP L-histidine ABC transporter, ATPase component AapP A3K86_RS01690 A3K86_RS21200
aapQ L-histidine ABC transporter, permease component 1 (AapQ) A3K86_RS01700 A3K86_RS21185
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 A3K86_RS21195 A3K86_RS01790
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 A3K86_RS13005 A3K86_RS15565
Ac3H11_2560 L-histidine ABC transporter, ATPase component A3K86_RS02885 A3K86_RS10595
Ac3H11_2561 L-histidine ABC transporter, permease component 1
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA A3K86_RS21200 A3K86_RS01690
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component A3K86_RS13005
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 A3K86_RS01790 A3K86_RS13010
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 A3K86_RS01785 A3K86_RS13015
BPHYT_RS24015 L-histidine ABC transporter, ATPase component A3K86_RS13000 A3K86_RS01690
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) A3K86_RS19745
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) A3K86_RS04635 A3K86_RS13000
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ A3K86_RS13005 A3K86_RS01795
hisM L-histidine ABC transporter, permease component 1 (HisM) A3K86_RS13015 A3K86_RS01785
hisP L-histidine ABC transporter, ATPase component HisP A3K86_RS13000 A3K86_RS01690
hisQ L-histidine ABC transporter, permease component 2 (HisQ) A3K86_RS13010 A3K86_RS01790
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) A3K86_RS10225 A3K86_RS12240
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC)
natD L-histidine ABC transporter, permease component 2 (NatD)
natE L-histidine ABC transporter, ATPase component 2 (NatE) A3K86_RS10225 A3K86_RS04635
PA5503 L-histidine ABC transporter, ATPase component A3K86_RS12240 A3K86_RS21200
PA5504 L-histidine ABC transporter, permease component A3K86_RS12245
PA5505 L-histidine ABC transporter, substrate-binding component A3K86_RS12250
permease L-histidine permease
PTR2 L-histidine:H+ symporter
S15A3 L-histidine transporter
SLC38A3 L-histidine:Na+ symporter

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

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