GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Malonomonas rubra DSM 5091

Best path

aapJ, aapQ, aapM, aapP, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ L-histidine ABC transporter, substrate-binding component AapJ BUB13_RS11680
aapQ L-histidine ABC transporter, permease component 1 (AapQ) BUB13_RS11685 BUB13_RS12685
aapM L-histidine ABC transporter, permease component 2 (AapM) BUB13_RS11690 BUB13_RS17605
aapP L-histidine ABC transporter, ATPase component AapP BUB13_RS11695 BUB13_RS17610
hutH histidine ammonia-lyase
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase
Alternative steps:
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 BUB13_RS17605 BUB13_RS12685
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 BUB13_RS17600
Ac3H11_2560 L-histidine ABC transporter, ATPase component BUB13_RS11050 BUB13_RS04110
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 BUB13_RS17610 BUB13_RS11695
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component
BPHYT_RS24005 L-histidine ABC transporter, permease component 1
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 BUB13_RS12685 BUB13_RS17605
BPHYT_RS24015 L-histidine ABC transporter, ATPase component BUB13_RS17610 BUB13_RS11695
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BUB13_RS01985
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BUB13_RS01980 BUB13_RS10000
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BUB13_RS01975 BUB13_RS09995
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BUB13_RS01970 BUB13_RS12770
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BUB13_RS01965 BUB13_RS09985
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ BUB13_RS17600
hisM L-histidine ABC transporter, permease component 1 (HisM) BUB13_RS17605 BUB13_RS12685
hisP L-histidine ABC transporter, ATPase component HisP BUB13_RS11695 BUB13_RS17610
hisQ L-histidine ABC transporter, permease component 2 (HisQ) BUB13_RS17605 BUB13_RS12685
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV BUB13_RS11050 BUB13_RS17610
hutW L-histidine ABC transporter, permease component HutW BUB13_RS11055
hutX L-histidine ABC transporter, substrate-binding component HutX
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) BUB13_RS12770 BUB13_RS11895
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) BUB13_RS10000 BUB13_RS12790
natE L-histidine ABC transporter, ATPase component 2 (NatE) BUB13_RS09985 BUB13_RS01965
PA5503 L-histidine ABC transporter, ATPase component BUB13_RS17610 BUB13_RS11695
PA5504 L-histidine ABC transporter, permease component
PA5505 L-histidine ABC transporter, substrate-binding component
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 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