GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Desulfovibrio vulgaris Hildenborough

Best path

permease, 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
permease L-histidine permease
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 DVU2342
aapM L-histidine ABC transporter, permease component 2 (AapM) DVU0751 DVU2340
aapP L-histidine ABC transporter, ATPase component AapP DVU0753 DVU2343
aapQ L-histidine ABC transporter, permease component 1 (AapQ) DVU2341 DVU0967
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 DVU0106 DVU1237
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 DVU0107 DVU0966
Ac3H11_2560 L-histidine ABC transporter, ATPase component DVU3161 DVU0098
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 DVU0105 DVU0753
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 DVU0387 DVU0967
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 DVU0389 DVU0674
BPHYT_RS24015 L-histidine ABC transporter, ATPase component DVU0105 DVU0968
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC DVU0547 DVU0712
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) DVU0548 DVU0713
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) DVU0549 DVU0714
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) DVU0550 DVU0715
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) DVU0551 DVU0716
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ DVU0386 DVU1238
hisM L-histidine ABC transporter, permease component 1 (HisM) DVU0387 DVU0967
hisP L-histidine ABC transporter, ATPase component HisP DVU0105 DVU1236
hisQ L-histidine ABC transporter, permease component 2 (HisQ) DVU0967 DVU0387
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV DVU2299 DVU1236
hutW L-histidine ABC transporter, permease component HutW DVU2298
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) DVU2741 DVU0715
natB L-histidine ABC transporter, substrate-binding component NatB
natC L-histidine ABC transporter, permease component 1 (NatC) DVU0549
natD L-histidine ABC transporter, permease component 2 (NatD) DVU0713 DVU0548
natE L-histidine ABC transporter, ATPase component 2 (NatE) DVU0551 DVU0716
PA5503 L-histidine ABC transporter, ATPase component DVU1236 DVU2343
PA5504 L-histidine ABC transporter, permease component
PA5505 L-histidine ABC transporter, substrate-binding component
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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