GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Pseudomonas stutzeri RCH2

Best path

hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, 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
hisP L-histidine ABC transporter, ATPase component HisP Psest_0139 Psest_0016
hisM L-histidine ABC transporter, permease component 1 (HisM) Psest_0136 Psest_0018
hisQ L-histidine ABC transporter, permease component 2 (HisQ) Psest_0137 Psest_0018
hisJ L-histidine ABC transporter, substrate-binding component HisJ Psest_0138
hutH histidine ammonia-lyase Psest_3695
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ Psest_3163
aapM L-histidine ABC transporter, permease component 2 (AapM) Psest_3161 Psest_0018
aapP L-histidine ABC transporter, ATPase component AapP Psest_3160 Psest_0139
aapQ L-histidine ABC transporter, permease component 1 (AapQ) Psest_3162
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 Psest_0017 Psest_0018
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component Psest_2365 Psest_1398
Ac3H11_2561 L-histidine ABC transporter, permease component 1 Psest_2364 Psest_2346
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA Psest_3160 Psest_0139
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component Psest_0138
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 Psest_0137 Psest_0136
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 Psest_0136 Psest_0137
BPHYT_RS24015 L-histidine ABC transporter, ATPase component Psest_0139 Psest_0016
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Psest_1312
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Psest_1311 Psest_1092
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Psest_1310
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Psest_1309 Psest_3853
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Psest_1308 Psest_0563
Ga0059261_1577 L-histidine transporter
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV Psest_4314 Psest_4282
hutW L-histidine ABC transporter, permease component HutW
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) Psest_1309 Psest_1089
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) Psest_1311 Psest_1092
natE L-histidine ABC transporter, ATPase component 2 (NatE) Psest_1308 Psest_0563
PA5503 L-histidine ABC transporter, ATPase component Psest_4314 Psest_0016
PA5504 L-histidine ABC transporter, permease component Psest_4315
PA5505 L-histidine ABC transporter, substrate-binding component Psest_4316
permease L-histidine permease Psest_1697
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.

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, 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