GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Ruegeria conchae TW15

Best path

aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'

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
aapJ L-histidine ABC transporter, substrate-binding component AapJ G7G_RS0100225
aapQ L-histidine ABC transporter, permease component 1 (AapQ) G7G_RS0100230
aapM L-histidine ABC transporter, permease component 2 (AapM) G7G_RS0100235
aapP L-histidine ABC transporter, ATPase component AapP G7G_RS0100240 G7G_RS0111050
hutH histidine ammonia-lyase G7G_RS0109010
hutU urocanase G7G_RS0109020
hutI imidazole-5-propionate hydrolase G7G_RS0109005
hutF N-formiminoglutamate deiminase G7G_RS0109000
hutG' N-formylglutamate amidohydrolase G7G_RS0109015
Alternative steps:
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 G7G_RS0111055 G7G_RS0111530
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component G7G_RS0111350 G7G_RS0105800
Ac3H11_2561 L-histidine ABC transporter, permease component 1 G7G_RS0111345
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA G7G_RS0100240 G7G_RS0105150
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) G7G_RS0111055 G7G_RS0111530
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 G7G_RS0101320 G7G_RS0100235
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 G7G_RS0111530
BPHYT_RS24015 L-histidine ABC transporter, ATPase component G7G_RS0105150 G7G_RS0100240
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) G7G_RS0101020 G7G_RS0107140
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) G7G_RS0118395 G7G_RS0116930
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) G7G_RS0118410 G7G_RS0107130
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) G7G_RS0115355 G7G_RS0107125
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ G7G_RS0105145 G7G_RS0111525
hisM L-histidine ABC transporter, permease component 1 (HisM) G7G_RS0105135 G7G_RS0111055
hisP L-histidine ABC transporter, ATPase component HisP G7G_RS0105150 G7G_RS0111050
hisQ L-histidine ABC transporter, permease component 2 (HisQ) G7G_RS0111530 G7G_RS0105140
hutG N-formiminoglutamate formiminohydrolase G7G_RS0101705
hutV L-histidine ABC transporter, ATPase component HutV G7G_RS0117040 G7G_RS0115845
hutW L-histidine ABC transporter, permease component HutW G7G_RS0117035 G7G_RS0113480
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) G7G_RS0107430 G7G_RS0107130
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) G7G_RS0107445 G7G_RS0107140
natE L-histidine ABC transporter, ATPase component 2 (NatE) G7G_RS0107435 G7G_RS0107125
PA5503 L-histidine ABC transporter, ATPase component G7G_RS0111050 G7G_RS0101315
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 24 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:

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