GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Marinobacter adhaerens HP15

Best path

PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG

Also see fitness data for the top candidates

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PA5503 L-histidine ABC transporter, ATPase component HP15_3903 HP15_2193
PA5504 L-histidine ABC transporter, permease component HP15_3904
PA5505 L-histidine ABC transporter, substrate-binding component HP15_3905
hutH histidine ammonia-lyase
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ HP15_2196
aapM L-histidine ABC transporter, permease component 2 (AapM) HP15_2194 HP15_2919
aapP L-histidine ABC transporter, ATPase component AapP HP15_2193 HP15_2920
aapQ L-histidine ABC transporter, permease component 1 (AapQ) HP15_2195 HP15_2919
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 HP15_1420 HP15_2919
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 HP15_2918 HP15_3031
Ac3H11_2560 L-histidine ABC transporter, ATPase component HP15_1014 HP15_939
Ac3H11_2561 L-histidine ABC transporter, permease component 1 HP15_3158
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA HP15_2920 HP15_3030
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 HP15_3032 HP15_2919
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 HP15_3033 HP15_3032
BPHYT_RS24015 L-histidine ABC transporter, ATPase component HP15_3030 HP15_2920
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC HP15_3055
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) HP15_3056 HP15_2706
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) HP15_3057 HP15_4097
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) HP15_3058 HP15_4095
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) HP15_3059 HP15_2703
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ HP15_3031 HP15_2918
hisM L-histidine ABC transporter, permease component 1 (HisM) HP15_3033 HP15_3032
hisP L-histidine ABC transporter, ATPase component HisP HP15_3030 HP15_2920
hisQ L-histidine ABC transporter, permease component 2 (HisQ) HP15_3032 HP15_2919
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV HP15_3298 HP15_994
hutW L-histidine ABC transporter, permease component HutW HP15_3297 HP15_995
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) HP15_2704 HP15_3058
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) HP15_3056
natE L-histidine ABC transporter, ATPase component 2 (NatE) HP15_3059 HP15_2703
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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