GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

hisP, hisM, hisQ, hisJ, 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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hisP L-histidine ABC transporter, ATPase component HisP Pf6N2E2_3855 Pf6N2E2_5663
hisM L-histidine ABC transporter, permease component 1 (HisM) Pf6N2E2_3858 Pf6N2E2_2960
hisQ L-histidine ABC transporter, permease component 2 (HisQ) Pf6N2E2_3857 Pf6N2E2_2959
hisJ L-histidine ABC transporter, substrate-binding component HisJ Pf6N2E2_3856 Pf6N2E2_1098
hutH histidine ammonia-lyase Pf6N2E2_3799 Pf6N2E2_3800
hutU urocanase Pf6N2E2_3805
hutI imidazole-5-propionate hydrolase Pf6N2E2_3798
hutF N-formiminoglutamate deiminase Pf6N2E2_3808
hutG' N-formylglutamate amidohydrolase Pf6N2E2_3797
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ Pf6N2E2_5402
aapM L-histidine ABC transporter, permease component 2 (AapM) Pf6N2E2_5404 Pf6N2E2_5568
aapP L-histidine ABC transporter, ATPase component AapP Pf6N2E2_5405 Pf6N2E2_5567
aapQ L-histidine ABC transporter, permease component 1 (AapQ) Pf6N2E2_5403
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 Pf6N2E2_3920 Pf6N2E2_2052
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 Pf6N2E2_3919 Pf6N2E2_5395
Ac3H11_2560 L-histidine ABC transporter, ATPase component Pf6N2E2_3975 Pf6N2E2_2777
Ac3H11_2561 L-histidine ABC transporter, permease component 1 Pf6N2E2_3911 Pf6N2E2_2776
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA Pf6N2E2_2962 Pf6N2E2_5663
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) Pf6N2E2_1799
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component Pf6N2E2_5660 Pf6N2E2_3856
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 Pf6N2E2_2959 Pf6N2E2_3857
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 Pf6N2E2_5662 Pf6N2E2_3858
BPHYT_RS24015 L-histidine ABC transporter, ATPase component Pf6N2E2_3855 Pf6N2E2_5663
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Pf6N2E2_3580 Pf6N2E2_2921
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Pf6N2E2_3579 Pf6N2E2_2923
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Pf6N2E2_2924 Pf6N2E2_3578
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Pf6N2E2_3577 Pf6N2E2_2925
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Pf6N2E2_3576 Pf6N2E2_2926
Ga0059261_1577 L-histidine transporter
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV Pf6N2E2_3801 Pf6N2E2_4681
hutW L-histidine ABC transporter, permease component HutW Pf6N2E2_3802 Pf6N2E2_4682
hutX L-histidine ABC transporter, substrate-binding component HutX Pf6N2E2_3803 Pf6N2E2_530
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) Pf6N2E2_2925 Pf6N2E2_1705
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) Pf6N2E2_3579 Pf6N2E2_3548
natE L-histidine ABC transporter, ATPase component 2 (NatE) Pf6N2E2_2926 Pf6N2E2_3576
PA5503 L-histidine ABC transporter, ATPase component Pf6N2E2_4172 Pf6N2E2_3927
PA5504 L-histidine ABC transporter, permease component Pf6N2E2_4173 Pf6N2E2_3928
PA5505 L-histidine ABC transporter, substrate-binding component Pf6N2E2_4174 Pf6N2E2_3953
permease L-histidine permease Pf6N2E2_5459 Pf6N2E2_5633
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