GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Escherichia coli BW25113

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hisP L-histidine ABC transporter, ATPase component HisP b2306 b1917
hisM L-histidine ABC transporter, permease component 1 (HisM) b2307 b0861
hisQ L-histidine ABC transporter, permease component 2 (HisQ) b2308 b0862
hisJ L-histidine ABC transporter, substrate-binding component HisJ b2309 b2310
hutH histidine ammonia-lyase
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutG N-formiminoglutamate formiminohydrolase
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) b3270 b1918
aapP L-histidine ABC transporter, ATPase component AapP b3271 b0652
aapQ L-histidine ABC transporter, permease component 1 (AapQ) b3269
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 b0810 b1918
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 b0811 b1920
Ac3H11_2560 L-histidine ABC transporter, ATPase component b0366 b1126
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 b2306 b3271
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 b2308 b0862
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 b0861 b1918
BPHYT_RS24015 L-histidine ABC transporter, ATPase component b2306 b1917
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC b3460 b3458
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) b3457
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) b3456
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) b3455
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) b3454 b3455
Ga0059261_1577 L-histidine transporter
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV b2677 b2129
hutW L-histidine ABC transporter, permease component HutW b2678 b2130
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) b3455 b3201
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)
natE L-histidine ABC transporter, ATPase component 2 (NatE) b3454 b3455
PA5503 L-histidine ABC transporter, ATPase component b0199 b2306
PA5504 L-histidine ABC transporter, permease component b0198
PA5505 L-histidine ABC transporter, substrate-binding component b0197 b3661
permease L-histidine permease b0402 b2156
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