GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Pseudomonas fluorescens GW456-L13

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hisP L-histidine ABC transporter, ATPase component HisP PfGW456L13_376 PfGW456L13_1967
hisM L-histidine ABC transporter, permease component 1 (HisM) PfGW456L13_379 PfGW456L13_385
hisQ L-histidine ABC transporter, permease component 2 (HisQ) PfGW456L13_378 PfGW456L13_4636
hisJ L-histidine ABC transporter, substrate-binding component HisJ PfGW456L13_377 PfGW456L13_1692
hutH histidine ammonia-lyase PfGW456L13_320 PfGW456L13_321
hutU urocanase PfGW456L13_326
hutI imidazole-5-propionate hydrolase PfGW456L13_317
hutF N-formiminoglutamate deiminase PfGW456L13_330
hutG' N-formylglutamate amidohydrolase PfGW456L13_316
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ PfGW456L13_1698
aapM L-histidine ABC transporter, permease component 2 (AapM) PfGW456L13_1700 PfGW456L13_4772
aapP L-histidine ABC transporter, ATPase component AapP PfGW456L13_1701 PfGW456L13_4773
aapQ L-histidine ABC transporter, permease component 1 (AapQ) PfGW456L13_1699
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 PfGW456L13_445 PfGW456L13_3607
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 PfGW456L13_444 PfGW456L13_1692
Ac3H11_2560 L-histidine ABC transporter, ATPase component PfGW456L13_1401 PfGW456L13_2816
Ac3H11_2561 L-histidine ABC transporter, permease component 1 PfGW456L13_1400 PfGW456L13_433
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA PfGW456L13_4639 PfGW456L13_386
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component PfGW456L13_3699 PfGW456L13_377
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 PfGW456L13_384 PfGW456L13_378
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 PfGW456L13_1966 PfGW456L13_379
BPHYT_RS24015 L-histidine ABC transporter, ATPase component PfGW456L13_376 PfGW456L13_1967
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC PfGW456L13_124 PfGW456L13_4606
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PfGW456L13_123 PfGW456L13_4608
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PfGW456L13_4609 PfGW456L13_122
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PfGW456L13_121 PfGW456L13_4610
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PfGW456L13_120 PfGW456L13_4611
Ga0059261_1577 L-histidine transporter
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV PfGW456L13_322 PfGW456L13_3150
hutW L-histidine ABC transporter, permease component HutW PfGW456L13_323 PfGW456L13_1087
hutX L-histidine ABC transporter, substrate-binding component HutX PfGW456L13_324 PfGW456L13_3631
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) PfGW456L13_4610 PfGW456L13_84
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) PfGW456L13_4608
natE L-histidine ABC transporter, ATPase component 2 (NatE) PfGW456L13_4611 PfGW456L13_120
PA5503 L-histidine ABC transporter, ATPase component PfGW456L13_602 PfGW456L13_453
PA5504 L-histidine ABC transporter, permease component PfGW456L13_603 PfGW456L13_454
PA5505 L-histidine ABC transporter, substrate-binding component PfGW456L13_604 PfGW456L13_464
permease L-histidine permease PfGW456L13_318 PfGW456L13_4790
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