GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Phaeobacter inhibens BS107

Best path

hutV, hutW, hutX, hutH, hutU, hutI, hutF, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hutV L-histidine ABC transporter, ATPase component HutV PGA1_c25590 PGA1_c22780
hutW L-histidine ABC transporter, permease component HutW PGA1_c22790 PGA1_c25580
hutX L-histidine ABC transporter, substrate-binding component HutX PGA1_c25570 PGA1_c22800
hutH histidine ammonia-lyase PGA1_c36340
hutU urocanase PGA1_c36320
hutI imidazole-5-propionate hydrolase PGA1_c36350
hutF N-formiminoglutamate deiminase PGA1_c36360
hutG' N-formylglutamate amidohydrolase PGA1_c36330 PGA1_c32480
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ PGA1_c01980
aapM L-histidine ABC transporter, permease component 2 (AapM) PGA1_c02000 PGA1_c26600
aapP L-histidine ABC transporter, ATPase component AapP PGA1_c02010 PGA1_262p02350
aapQ L-histidine ABC transporter, permease component 1 (AapQ) PGA1_c01990 PGA1_65p00120
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 PGA1_65p00120 PGA1_c26600
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 PGA1_65p00110
Ac3H11_2560 L-histidine ABC transporter, ATPase component PGA1_c12860 PGA1_c28320
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 PGA1_c02010 PGA1_262p02350
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 PGA1_262p02370
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 PGA1_262p02380 PGA1_65p00120
BPHYT_RS24015 L-histidine ABC transporter, ATPase component PGA1_262p02350 PGA1_c11580
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) PGA1_c02590
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) PGA1_c32620 PGA1_c02610
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PGA1_c02620 PGA1_c32560
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ PGA1_262p02360 PGA1_c11570
hisM L-histidine ABC transporter, permease component 1 (HisM) PGA1_c11550 PGA1_262p02380
hisP L-histidine ABC transporter, ATPase component HisP PGA1_262p02350 PGA1_c11580
hisQ L-histidine ABC transporter, permease component 2 (HisQ) PGA1_262p02370 PGA1_c26600
hutG N-formiminoglutamate formiminohydrolase
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) PGA1_c15910 PGA1_c02610
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) PGA1_c15940
natE L-histidine ABC transporter, ATPase component 2 (NatE) PGA1_c15920 PGA1_c02620
PA5503 L-histidine ABC transporter, ATPase component PGA1_c25590 PGA1_262p02350
PA5504 L-histidine ABC transporter, permease component
PA5505 L-histidine ABC transporter, substrate-binding component
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 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