GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Klebsiella michiganensis M5al

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hisP L-histidine ABC transporter, ATPase component HisP BWI76_RS20320 BWI76_RS07590
hisM L-histidine ABC transporter, permease component 1 (HisM) BWI76_RS20325 BWI76_RS19230
hisQ L-histidine ABC transporter, permease component 2 (HisQ) BWI76_RS20330 BWI76_RS19235
hisJ L-histidine ABC transporter, substrate-binding component HisJ BWI76_RS20335 BWI76_RS07345
hutH histidine ammonia-lyase BWI76_RS08740
hutU urocanase BWI76_RS08735
hutI imidazole-5-propionate hydrolase BWI76_RS08720
hutG N-formiminoglutamate formiminohydrolase BWI76_RS08725
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) BWI76_RS18355 BWI76_RS13550
aapP L-histidine ABC transporter, ATPase component AapP BWI76_RS08095 BWI76_RS08965
aapQ L-histidine ABC transporter, permease component 1 (AapQ) BWI76_RS08100
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 BWI76_RS10375 BWI76_RS08970
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 BWI76_RS08975 BWI76_RS14445
Ac3H11_2560 L-histidine ABC transporter, ATPase component BWI76_RS16840 BWI76_RS05870
Ac3H11_2561 L-histidine ABC transporter, permease component 1 BWI76_RS06075 BWI76_RS13965
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1 BWI76_RS22885
bgtA L-histidine ABC transporter, ATPase component BgtA BWI76_RS16795 BWI76_RS20320
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component BWI76_RS18365
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 BWI76_RS20330 BWI76_RS19235
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 BWI76_RS09505 BWI76_RS18355
BPHYT_RS24015 L-histidine ABC transporter, ATPase component BWI76_RS20320 BWI76_RS16795
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BWI76_RS26350 BWI76_RS26365
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BWI76_RS26345 BWI76_RS07280
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BWI76_RS26340 BWI76_RS07275
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BWI76_RS26335 BWI76_RS07270
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BWI76_RS26330 BWI76_RS05975
Ga0059261_1577 L-histidine transporter
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV BWI76_RS22065 BWI76_RS17620
hutW L-histidine ABC transporter, permease component HutW BWI76_RS22070 BWI76_RS15035
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) BWI76_RS26335 BWI76_RS05980
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) BWI76_RS26345 BWI76_RS05990
natE L-histidine ABC transporter, ATPase component 2 (NatE) BWI76_RS26330 BWI76_RS05975
PA5503 L-histidine ABC transporter, ATPase component BWI76_RS05365 BWI76_RS16675
PA5504 L-histidine ABC transporter, permease component BWI76_RS16665 BWI76_RS15035
PA5505 L-histidine ABC transporter, substrate-binding component BWI76_RS16670 BWI76_RS15025
permease L-histidine permease BWI76_RS08745 BWI76_RS06245
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