GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Pseudomonas fluorescens FW300-N2C3

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 AO356_09895 AO356_18715
hisM L-histidine ABC transporter, permease component 1 (HisM) AO356_09910 AO356_27110
hisQ L-histidine ABC transporter, permease component 2 (HisQ) AO356_09905 AO356_27115
hisJ L-histidine ABC transporter, substrate-binding component HisJ AO356_09900 AO356_23515
hutH histidine ammonia-lyase AO356_09605 AO356_09600
hutU urocanase AO356_09630
hutI imidazole-5-propionate hydrolase AO356_09595
hutF N-formiminoglutamate deiminase AO356_09645
hutG' N-formylglutamate amidohydrolase AO356_09590
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ AO356_17380
aapM L-histidine ABC transporter, permease component 2 (AapM) AO356_17390 AO356_29675
aapP L-histidine ABC transporter, ATPase component AapP AO356_17395 AO356_18215
aapQ L-histidine ABC transporter, permease component 1 (AapQ) AO356_17385 AO356_29650
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 AO356_29650 AO356_10240
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 AO356_10235 AO356_17350
Ac3H11_2560 L-histidine ABC transporter, ATPase component AO356_21790 AO356_29555
Ac3H11_2561 L-histidine ABC transporter, permease component 1 AO356_10200 AO356_21785
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA AO356_05515 AO356_27105
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) AO356_29675
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component AO356_29765 AO356_01470
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 AO356_29785 AO356_27115
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 AO356_29790 AO356_18710
BPHYT_RS24015 L-histidine ABC transporter, ATPase component AO356_09895 AO356_18715
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC AO356_08500 AO356_05320
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AO356_08495 AO356_05325
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AO356_05330 AO356_08490
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) AO356_08485 AO356_05335
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) AO356_08480 AO356_05340
Ga0059261_1577 L-histidine transporter
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV AO356_09610 AO356_09255
hutW L-histidine ABC transporter, permease component HutW AO356_09615 AO356_13810
hutX L-histidine ABC transporter, substrate-binding component HutX AO356_09620 AO356_23245
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) AO356_05335 AO356_29020
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) AO356_08495 AO356_08345
natE L-histidine ABC transporter, ATPase component 2 (NatE) AO356_05340 AO356_08480
PA5503 L-histidine ABC transporter, ATPase component AO356_11510 AO356_10275
PA5504 L-histidine ABC transporter, permease component AO356_11515 AO356_10280
PA5505 L-histidine ABC transporter, substrate-binding component AO356_11520 AO356_10425
permease L-histidine permease AO356_17670 AO356_18530
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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