GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Dinoroseobacter shibae DFL-12

Best path

aapJ, aapQ, aapM, aapP, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ L-histidine ABC transporter, substrate-binding component AapJ Dshi_0318
aapQ L-histidine ABC transporter, permease component 1 (AapQ) Dshi_0319
aapM L-histidine ABC transporter, permease component 2 (AapM) Dshi_0320
aapP L-histidine ABC transporter, ATPase component AapP Dshi_0321 Dshi_2221
hutH histidine ammonia-lyase
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase
Alternative steps:
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component Dshi_1371 Dshi_1383
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 Dshi_0321 Dshi_2221
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 Dshi_2223
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 Dshi_0320
BPHYT_RS24015 L-histidine ABC transporter, ATPase component Dshi_2221 Dshi_0321
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) Dshi_3725 Dshi_0861
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Dshi_0379
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Dshi_0375 Dshi_3727
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Dshi_0381 Dshi_1400
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ Dshi_2222
hisM L-histidine ABC transporter, permease component 1 (HisM) Dshi_2224 Dshi_0320
hisP L-histidine ABC transporter, ATPase component HisP Dshi_2221 Dshi_0321
hisQ L-histidine ABC transporter, permease component 2 (HisQ) Dshi_2223
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase Dshi_0386
hutV L-histidine ABC transporter, ATPase component HutV Dshi_1437 Dshi_1055
hutW L-histidine ABC transporter, permease component HutW Dshi_1436
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) Dshi_1981 Dshi_1521
natB L-histidine ABC transporter, substrate-binding component NatB Dshi_1977
natC L-histidine ABC transporter, permease component 1 (NatC)
natD L-histidine ABC transporter, permease component 2 (NatD) Dshi_1518 Dshi_1979
natE L-histidine ABC transporter, ATPase component 2 (NatE) Dshi_1980 Dshi_1520
PA5503 L-histidine ABC transporter, ATPase component Dshi_1437 Dshi_0321
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.

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, 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