GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Sinorhizobium meliloti 1021

Best path

braC, braD, braE, braF, braG, 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
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC SMc01946 SMc00078
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) SMc01951 SMc02359
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) SMc01950
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) SMc01949 SMc02357
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) SMc01948 SMc02358
hutH histidine ammonia-lyase SM_b21165 SMc00669
hutU urocanase SM_b21163
hutI imidazole-5-propionate hydrolase SM_b21166
hutF N-formiminoglutamate deiminase SMc00673
hutG' N-formylglutamate amidohydrolase SM_b21164 SMc04043
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ SMc02118 SMc00676
aapM L-histidine ABC transporter, permease component 2 (AapM) SMc02120 SMc03865
aapP L-histidine ABC transporter, ATPase component AapP SMc02121 SMc03135
aapQ L-histidine ABC transporter, permease component 1 (AapQ) SMc02119 SMc03865
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 SMc03893 SM_b20430
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 SMc03891 SM_b20706
Ac3H11_2560 L-histidine ABC transporter, ATPase component SMc02346 SM_b20569
Ac3H11_2561 L-histidine ABC transporter, permease component 1 SM_b21528 SM_b20571
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA SM_b20266 SMc03135
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component SM_b20706 SMc00140
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 SMc00139 SMc02258
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 SMa0492 SMc02257
BPHYT_RS24015 L-histidine ABC transporter, ATPase component SMc02260 SMa2195
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ SM_b20706 SMc00140
hisM L-histidine ABC transporter, permease component 1 (HisM) SMa0492 SMc00138
hisP L-histidine ABC transporter, ATPase component HisP SMc02260 SM_b21138
hisQ L-histidine ABC transporter, permease component 2 (HisQ) SMc02258 SMc00139
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV SMc00670 SMc04439
hutW L-histidine ABC transporter, permease component HutW SMc00671 SMc02379
hutX L-histidine ABC transporter, substrate-binding component HutX SMc00672 SMc02378
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) SMc03120 SMc02357
natB L-histidine ABC transporter, substrate-binding component NatB SMc01946
natC L-histidine ABC transporter, permease component 1 (NatC)
natD L-histidine ABC transporter, permease component 2 (NatD) SM_b20604 SMc03118
natE L-histidine ABC transporter, ATPase component 2 (NatE) SMc01948 SMc02358
PA5503 L-histidine ABC transporter, ATPase component SMc03159 SM_b20427
PA5504 L-histidine ABC transporter, permease component SMc03158
PA5505 L-histidine ABC transporter, substrate-binding component SMc03157
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, 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