GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Pseudomonas fluorescens FW300-N2E3

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 AO353_12000 AO353_28150
hisM L-histidine ABC transporter, permease component 1 (HisM) AO353_11985 AO353_25650
hisQ L-histidine ABC transporter, permease component 2 (HisQ) AO353_11990 AO353_01535
hisJ L-histidine ABC transporter, substrate-binding component HisJ AO353_11995 AO353_29015
hutH histidine ammonia-lyase AO353_12270 AO353_17725
hutU urocanase AO353_12250
hutI imidazole-5-propionate hydrolase AO353_12280
hutF N-formiminoglutamate deiminase AO353_12235
hutG' N-formylglutamate amidohydrolase AO353_12285
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ AO353_04615
aapM L-histidine ABC transporter, permease component 2 (AapM) AO353_04605 AO353_12325
aapP L-histidine ABC transporter, ATPase component AapP AO353_04600 AO353_16275
aapQ L-histidine ABC transporter, permease component 1 (AapQ) AO353_04610
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 AO353_12325 AO353_24425
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 AO353_11675 AO353_04645
Ac3H11_2560 L-histidine ABC transporter, ATPase component AO353_15055 AO353_23185
Ac3H11_2561 L-histidine ABC transporter, permease component 1 AO353_15050 AO353_11715
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA AO353_16950 AO353_01525
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) AO353_25590
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component AO353_17720 AO353_27970
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 AO353_17715 AO353_01535
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 AO353_17710 AO353_03045
BPHYT_RS24015 L-histidine ABC transporter, ATPase component AO353_17705 AO353_28150
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC AO353_13340 AO353_17125
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AO353_13345 AO353_17120
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AO353_17115 AO353_13350
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AO353_13355 AO353_17110
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AO353_13360 AO353_17105
Ga0059261_1577 L-histidine transporter
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV AO353_12265 AO353_07790
hutW L-histidine ABC transporter, permease component HutW AO353_12260 AO353_07785
hutX L-histidine ABC transporter, substrate-binding component HutX AO353_21435
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) AO353_17110 AO353_05175
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) AO353_17120
natE L-histidine ABC transporter, ATPase component 2 (NatE) AO353_17105 AO353_13360
PA5503 L-histidine ABC transporter, ATPase component AO353_10890 AO353_11635
PA5504 L-histidine ABC transporter, permease component AO353_10885 AO353_22195
PA5505 L-histidine ABC transporter, substrate-binding component AO353_10880 AO353_11595
permease L-histidine permease AO353_12275 AO353_16120
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