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

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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