GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Arcobacter nitrofigilis DSM 7299

Best path

PA5503, PA5504, PA5505, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PA5503 L-histidine ABC transporter, ATPase component ARNIT_RS05320 ARNIT_RS13775
PA5504 L-histidine ABC transporter, permease component ARNIT_RS13770
PA5505 L-histidine ABC transporter, substrate-binding component ARNIT_RS13765
hutH histidine ammonia-lyase ARNIT_RS11570
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase ARNIT_RS07020
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ ARNIT_RS02910
aapM L-histidine ABC transporter, permease component 2 (AapM) ARNIT_RS02900 ARNIT_RS16500
aapP L-histidine ABC transporter, ATPase component AapP ARNIT_RS02895 ARNIT_RS13590
aapQ L-histidine ABC transporter, permease component 1 (AapQ) ARNIT_RS02905
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 ARNIT_RS13580 ARNIT_RS01645
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component ARNIT_RS02045 ARNIT_RS06765
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 ARNIT_RS02895 ARNIT_RS13590
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 ARNIT_RS13580
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 ARNIT_RS01645 ARNIT_RS01650
BPHYT_RS24015 L-histidine ABC transporter, ATPase component ARNIT_RS01655 ARNIT_RS02895
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) ARNIT_RS06925 ARNIT_RS08960
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) ARNIT_RS06930 ARNIT_RS08955
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) ARNIT_RS08950 ARNIT_RS06935
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) ARNIT_RS08945 ARNIT_RS06940
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ
hisM L-histidine ABC transporter, permease component 1 (HisM) ARNIT_RS01645 ARNIT_RS16500
hisP L-histidine ABC transporter, ATPase component HisP ARNIT_RS01655 ARNIT_RS05320
hisQ L-histidine ABC transporter, permease component 2 (HisQ) ARNIT_RS13580 ARNIT_RS01645
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV ARNIT_RS01680 ARNIT_RS06765
hutW L-histidine ABC transporter, permease component HutW ARNIT_RS01685
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) ARNIT_RS08950 ARNIT_RS06935
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) ARNIT_RS08960 ARNIT_RS06925
natE L-histidine ABC transporter, ATPase component 2 (NatE) ARNIT_RS08945 ARNIT_RS06940
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