GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Pseudomonas putida KT2440

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 PP_0283 PP_4483
hisM L-histidine ABC transporter, permease component 1 (HisM) PP_0280 PP_4484
hisQ L-histidine ABC transporter, permease component 2 (HisQ) PP_0281 PP_4485
hisJ L-histidine ABC transporter, substrate-binding component HisJ PP_0282 PP_3593
hutH histidine ammonia-lyase PP_5032
hutU urocanase PP_5033
hutI imidazole-5-propionate hydrolase PP_5030
hutF N-formiminoglutamate deiminase PP_5036
hutG' N-formylglutamate amidohydrolase PP_5029
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ PP_1297
aapM L-histidine ABC transporter, permease component 2 (AapM) PP_1299 PP_5023
aapP L-histidine ABC transporter, ATPase component AapP PP_1300 PP_3597
aapQ L-histidine ABC transporter, permease component 1 (AapQ) PP_1298 PP_5023
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 PP_0226 PP_5023
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 PP_0227 PP_0282
Ac3H11_2560 L-histidine ABC transporter, ATPase component PP_3211 PP_0209
Ac3H11_2561 L-histidine ABC transporter, permease component 1 PP_0231 PP_0208
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA PP_3597 PP_1300
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component PP_0282 PP_4486
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 PP_0281 PP_4485
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 PP_0280 PP_4484
BPHYT_RS24015 L-histidine ABC transporter, ATPase component PP_0283 PP_4483
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC PP_4867 PP_1141
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) PP_1140 PP_4866
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PP_1139 PP_4865
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PP_4864 PP_1138
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PP_4863 PP_1137
Ga0059261_1577 L-histidine transporter
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV PP_0294 PP_2774
hutW L-histidine ABC transporter, permease component HutW PP_3559 PP_2774
hutX L-histidine ABC transporter, substrate-binding component HutX PP_3558
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) PP_1138 PP_2767
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) PP_1140 PP_0618
natE L-histidine ABC transporter, ATPase component 2 (NatE) PP_1137 PP_4863
PA5503 L-histidine ABC transporter, ATPase component PP_0114 PP_0220
PA5504 L-histidine ABC transporter, permease component PP_0113 PP_0219
PA5505 L-histidine ABC transporter, substrate-binding component PP_0112 PP_5165
permease L-histidine permease PP_5031 PP_1059
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 (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 paper from 2022 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