GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Synechococcus elongatus PCC 7942

Best path

natA, natB, natC, natD, natE, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-histidine ABC transporter, ATPase component 1 (NatA) Synpcc7942_1893 Synpcc7942_2493
natB L-histidine ABC transporter, substrate-binding component NatB Synpcc7942_1861
natC L-histidine ABC transporter, permease component 1 (NatC) Synpcc7942_1894
natD L-histidine ABC transporter, permease component 2 (NatD) Synpcc7942_2177 Synpcc7942_2495
natE L-histidine ABC transporter, ATPase component 2 (NatE) Synpcc7942_0815 Synpcc7942_2492
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 Synpcc7942_0246
aapM L-histidine ABC transporter, permease component 2 (AapM) Synpcc7942_0248
aapP L-histidine ABC transporter, ATPase component AapP Synpcc7942_0249 Synpcc7942_1680
aapQ L-histidine ABC transporter, permease component 1 (AapQ) Synpcc7942_0247
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component Synpcc7942_2105 Synpcc7942_1490
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 Synpcc7942_0249 Synpcc7942_1414
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
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 Synpcc7942_0248 Synpcc7942_0247
BPHYT_RS24015 L-histidine ABC transporter, ATPase component Synpcc7942_0249 Synpcc7942_1680
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) Synpcc7942_2495
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Synpcc7942_2494
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Synpcc7942_2493 Synpcc7942_1893
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Synpcc7942_2492 Synpcc7942_0815
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ
hisM L-histidine ABC transporter, permease component 1 (HisM) Synpcc7942_0248 Synpcc7942_0247
hisP L-histidine ABC transporter, ATPase component HisP Synpcc7942_0249 Synpcc7942_1414
hisQ L-histidine ABC transporter, permease component 2 (HisQ) Synpcc7942_0248
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV Synpcc7942_1680 Synpcc7942_1406
hutW L-histidine ABC transporter, permease component HutW
hutX L-histidine ABC transporter, substrate-binding component HutX
LAT2 L-histidine transporter
LHT L-histidine transporter
PA5503 L-histidine ABC transporter, ATPase component Synpcc7942_0249 Synpcc7942_1680
PA5504 L-histidine ABC transporter, permease component
PA5505 L-histidine ABC transporter, substrate-binding component
permease L-histidine permease
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, 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