GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Rhizorhabdus wittichii RW1

Best path

Ga0059261_1577, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Ga0059261_1577 L-histidine transporter SWIT_RS22305 SWIT_RS13040
hutH histidine ammonia-lyase SWIT_RS23385
hutU urocanase SWIT_RS23375
hutI imidazole-5-propionate hydrolase SWIT_RS23390
hutF N-formiminoglutamate deiminase SWIT_RS23395
hutG' N-formylglutamate amidohydrolase SWIT_RS23380
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ SWIT_RS13335
aapM L-histidine ABC transporter, permease component 2 (AapM) SWIT_RS13325 SWIT_RS13330
aapP L-histidine ABC transporter, ATPase component AapP SWIT_RS13320 SWIT_RS04010
aapQ L-histidine ABC transporter, permease component 1 (AapQ) SWIT_RS13330 SWIT_RS13325
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 SWIT_RS13325 SWIT_RS13330
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component SWIT_RS01355 SWIT_RS12715
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 SWIT_RS13320 SWIT_RS04010
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 SWIT_RS13320 SWIT_RS11865
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) SWIT_RS14705 SWIT_RS04010
hisJ L-histidine ABC transporter, substrate-binding component HisJ
hisM L-histidine ABC transporter, permease component 1 (HisM) SWIT_RS13325 SWIT_RS13330
hisP L-histidine ABC transporter, ATPase component HisP SWIT_RS13320 SWIT_RS00070
hisQ L-histidine ABC transporter, permease component 2 (HisQ)
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV SWIT_RS01355 SWIT_RS04010
hutW L-histidine ABC transporter, permease component HutW SWIT_RS04005 SWIT_RS12720
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) SWIT_RS14705 SWIT_RS09730
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) SWIT_RS14705 SWIT_RS01285
PA5503 L-histidine ABC transporter, ATPase component SWIT_RS13320 SWIT_RS04010
PA5504 L-histidine ABC transporter, permease component
PA5505 L-histidine ABC transporter, substrate-binding component
permease L-histidine permease SWIT_RS03485
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 Apr 09 2024. 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