GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Marivita geojedonensis DPG-138

Best path

hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hisP L-histidine ABC transporter, ATPase component HisP MGEO_RS08670 MGEO_RS13225
hisM L-histidine ABC transporter, permease component 1 (HisM) MGEO_RS13240 MGEO_RS07795
hisQ L-histidine ABC transporter, permease component 2 (HisQ) MGEO_RS13235 MGEO_RS07800
hisJ L-histidine ABC transporter, substrate-binding component HisJ MGEO_RS07805 MGEO_RS13230
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 MGEO_RS16990
aapM L-histidine ABC transporter, permease component 2 (AapM) MGEO_RS17000 MGEO_RS10180
aapP L-histidine ABC transporter, ATPase component AapP MGEO_RS17005 MGEO_RS07775
aapQ L-histidine ABC transporter, permease component 1 (AapQ) MGEO_RS16995
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 MGEO_RS10185 MGEO_RS10180
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 MGEO_RS07805
Ac3H11_2560 L-histidine ABC transporter, ATPase component MGEO_RS04720 MGEO_RS10530
Ac3H11_2561 L-histidine ABC transporter, permease component 1 MGEO_RS04715
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA MGEO_RS07775 MGEO_RS17005
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component MGEO_RS13230 MGEO_RS07805
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 MGEO_RS13235 MGEO_RS07800
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 MGEO_RS13240 MGEO_RS07795
BPHYT_RS24015 L-histidine ABC transporter, ATPase component MGEO_RS13225 MGEO_RS08670
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) MGEO_RS18500
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) MGEO_RS04005 MGEO_RS05255
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) MGEO_RS05250 MGEO_RS04030
Ga0059261_1577 L-histidine transporter
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase MGEO_RS04065
hutV L-histidine ABC transporter, ATPase component HutV MGEO_RS18525 MGEO_RS10720
hutW L-histidine ABC transporter, permease component HutW MGEO_RS10725 MGEO_RS18520
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) MGEO_RS19860 MGEO_RS14455
natB L-histidine ABC transporter, substrate-binding component NatB MGEO_RS14450
natC L-histidine ABC transporter, permease component 1 (NatC)
natD L-histidine ABC transporter, permease component 2 (NatD) MGEO_RS14465 MGEO_RS19850
natE L-histidine ABC transporter, ATPase component 2 (NatE) MGEO_RS14460 MGEO_RS19855
PA5503 L-histidine ABC transporter, ATPase component MGEO_RS10190 MGEO_RS16910
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