GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Chryseobacterium arthrosphaerae CC-VM-7

Best path

permease, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
permease L-histidine permease BBI00_RS13465
hutH histidine ammonia-lyase BBI00_RS00455 BBI00_RS19040
hutU urocanase BBI00_RS08420 BBI00_RS00465
hutI imidazole-5-propionate hydrolase BBI00_RS14525 BBI00_RS00460
hutG N-formiminoglutamate formiminohydrolase BBI00_RS14515
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM)
aapP L-histidine ABC transporter, ATPase component AapP BBI00_RS09790 BBI00_RS12055
aapQ L-histidine ABC transporter, permease component 1 (AapQ)
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 BBI00_RS20685 BBI00_RS12055
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 BBI00_RS09790 BBI00_RS20685
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
BPHYT_RS24015 L-histidine ABC transporter, ATPase component BBI00_RS09790 BBI00_RS12055
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)
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)
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BBI00_RS11725 BBI00_RS09520
Ga0059261_1577 L-histidine transporter BBI00_RS02720 BBI00_RS08080
hisJ L-histidine ABC transporter, substrate-binding component HisJ
hisM L-histidine ABC transporter, permease component 1 (HisM)
hisP L-histidine ABC transporter, ATPase component HisP BBI00_RS09790 BBI00_RS12055
hisQ L-histidine ABC transporter, permease component 2 (HisQ)
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV BBI00_RS20685 BBI00_RS09790
hutW L-histidine ABC transporter, permease component HutW BBI00_RS20680
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) BBI00_RS11725 BBI00_RS09790
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)
natE L-histidine ABC transporter, ATPase component 2 (NatE) BBI00_RS11725 BBI00_RS01845
PA5503 L-histidine ABC transporter, ATPase component BBI00_RS09790 BBI00_RS20685
PA5504 L-histidine ABC transporter, permease component BBI00_RS09795
PA5505 L-histidine ABC transporter, substrate-binding component BBI00_RS09800
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