GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Herbaspirillum seropedicae SmR1

Best path

PA5503, PA5504, PA5505, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PA5503 L-histidine ABC transporter, ATPase component HSERO_RS07850 HSERO_RS04980
PA5504 L-histidine ABC transporter, permease component HSERO_RS07845 HSERO_RS11635
PA5505 L-histidine ABC transporter, substrate-binding component HSERO_RS07840 HSERO_RS04970
hutH histidine ammonia-lyase HSERO_RS22680 HSERO_RS18505
hutU urocanase
hutI imidazole-5-propionate hydrolase
hutF N-formiminoglutamate deiminase HSERO_RS11455
hutG' N-formylglutamate amidohydrolase
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) HSERO_RS07530 HSERO_RS23030
aapP L-histidine ABC transporter, ATPase component AapP HSERO_RS17555 HSERO_RS19240
aapQ L-histidine ABC transporter, permease component 1 (AapQ) HSERO_RS19340 HSERO_RS17565
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 HSERO_RS11445 HSERO_RS05830
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 HSERO_RS11440 HSERO_RS17550
Ac3H11_2560 L-histidine ABC transporter, ATPase component HSERO_RS01865 HSERO_RS16975
Ac3H11_2561 L-histidine ABC transporter, permease component 1 HSERO_RS01860
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA HSERO_RS00320 HSERO_RS21250
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component HSERO_RS10775
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 HSERO_RS11445 HSERO_RS05830
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 HSERO_RS11445 HSERO_RS10770
BPHYT_RS24015 L-histidine ABC transporter, ATPase component HSERO_RS00320 HSERO_RS05835
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC HSERO_RS08270 HSERO_RS17350
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) HSERO_RS08275 HSERO_RS05960
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) HSERO_RS08280 HSERO_RS05965
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) HSERO_RS08285 HSERO_RS20055
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) HSERO_RS08290 HSERO_RS05975
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ HSERO_RS10775 HSERO_RS21615
hisM L-histidine ABC transporter, permease component 1 (HisM) HSERO_RS11445 HSERO_RS23035
hisP L-histidine ABC transporter, ATPase component HisP HSERO_RS00320 HSERO_RS05835
hisQ L-histidine ABC transporter, permease component 2 (HisQ) HSERO_RS05830 HSERO_RS00315
hutG N-formiminoglutamate formiminohydrolase HSERO_RS08555 HSERO_RS00305
hutV L-histidine ABC transporter, ATPase component HutV HSERO_RS08545 HSERO_RS04980
hutW L-histidine ABC transporter, permease component HutW HSERO_RS08540 HSERO_RS07845
hutX L-histidine ABC transporter, substrate-binding component HutX
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) HSERO_RS14705 HSERO_RS08285
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) HSERO_RS08275 HSERO_RS05960
natE L-histidine ABC transporter, ATPase component 2 (NatE) HSERO_RS06785 HSERO_RS08925
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