GapMind for catabolism of small carbon sources

 

Definition of L-histidine catabolism

As rules and steps, or see full text

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.

Steps

hisP: L-histidine ABC transporter, ATPase component HisP

hisM: L-histidine ABC transporter, permease component 1 (HisM)

hisQ: L-histidine ABC transporter, permease component 2 (HisQ)

hisJ: L-histidine ABC transporter, substrate-binding component HisJ

PA5503: L-histidine ABC transporter, ATPase component

PA5504: L-histidine ABC transporter, permease component

PA5505: L-histidine ABC transporter, substrate-binding component

Ac3H11_2562: L-histidine ABC transporter, substrate-binding component 1

Ac3H11_2561: L-histidine ABC transporter, permease component 1

Ac3H11_2560: L-histidine ABC transporter, ATPase component

Ac3H11_2555: L-histidine ABC transporter, substrate-binding component 2

Ac3H11_2554: ABC transporter for L-Histidine, permease component 2

natA: L-histidine ABC transporter, ATPase component 1 (NatA)

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)

aapJ: L-histidine ABC transporter, substrate-binding component AapJ

aapQ: L-histidine ABC transporter, permease component 1 (AapQ)

aapM: L-histidine ABC transporter, permease component 2 (AapM)

aapP: L-histidine ABC transporter, ATPase component AapP

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)

braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)

hutV: L-histidine ABC transporter, ATPase component HutV

hutW: L-histidine ABC transporter, permease component HutW

hutX: L-histidine ABC transporter, substrate-binding component HutX

bgtA: L-histidine ABC transporter, ATPase component BgtA

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

BPHYT_RS24015: L-histidine ABC transporter, ATPase component

permease: L-histidine permease

Ga0059261_1577: L-histidine transporter

S15A3: L-histidine transporter

LAT2: L-histidine transporter

LHT: L-histidine transporter

SLC38A3: L-histidine:Na+ symporter

PTR2: L-histidine:H+ symporter

hutH: histidine ammonia-lyase

hutU: urocanase

hutI: imidazole-5-propionate hydrolase

hutG: N-formiminoglutamate formiminohydrolase

hutF: N-formiminoglutamate deiminase

hutG': N-formylglutamate amidohydrolase

Links

Downloads

Related tools

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, 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