GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Dyella japonica UNC79MFTsu3.2

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PA5503 L-histidine ABC transporter, ATPase component N515DRAFT_1085 N515DRAFT_1562
PA5504 L-histidine ABC transporter, permease component N515DRAFT_1084
PA5505 L-histidine ABC transporter, substrate-binding component N515DRAFT_1083
hutH histidine ammonia-lyase N515DRAFT_2941
hutU urocanase N515DRAFT_0165
hutI imidazole-5-propionate hydrolase N515DRAFT_0142
hutF N-formiminoglutamate deiminase N515DRAFT_0145
hutG' N-formylglutamate amidohydrolase N515DRAFT_3725
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 N515DRAFT_1085 N515DRAFT_1562
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 N515DRAFT_1562 N515DRAFT_1085
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 N515DRAFT_1085 N515DRAFT_1562
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 N515DRAFT_1085 N515DRAFT_1562
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) N515DRAFT_3950 N515DRAFT_3588
Ga0059261_1577 L-histidine transporter N515DRAFT_2924 N515DRAFT_0606
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 N515DRAFT_1085 N515DRAFT_1562
hisQ L-histidine ABC transporter, permease component 2 (HisQ)
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV N515DRAFT_1562 N515DRAFT_1085
hutW L-histidine ABC transporter, permease component HutW
hutX L-histidine ABC transporter, substrate-binding component HutX
LAT2 L-histidine transporter N515DRAFT_4009
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) N515DRAFT_3950 N515DRAFT_1687
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) N515DRAFT_3950 N515DRAFT_1687
permease L-histidine permease N515DRAFT_2630 N515DRAFT_3653
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 (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 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