GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Rhodanobacter denitrificans 2APBS1

Best path

PA5503, PA5504, PA5505, 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
PA5503 L-histidine ABC transporter, ATPase component R2APBS1_RS13010 R2APBS1_RS17165
PA5504 L-histidine ABC transporter, permease component R2APBS1_RS13015
PA5505 L-histidine ABC transporter, substrate-binding component R2APBS1_RS13020
hutH histidine ammonia-lyase R2APBS1_RS07010
hutU urocanase R2APBS1_RS11450
hutI imidazole-5-propionate hydrolase R2APBS1_RS11535
hutF N-formiminoglutamate deiminase R2APBS1_RS11525
hutG' N-formylglutamate amidohydrolase R2APBS1_RS05715
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 R2APBS1_RS13010 R2APBS1_RS11520
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 R2APBS1_RS03925 R2APBS1_RS16135
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 R2APBS1_RS13010 R2APBS1_RS03925
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 R2APBS1_RS11520 R2APBS1_RS13010
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) R2APBS1_RS05195 R2APBS1_RS17250
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) R2APBS1_RS15240 R2APBS1_RS13570
Ga0059261_1577 L-histidine transporter R2APBS1_RS06770 R2APBS1_RS06765
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 R2APBS1_RS13010 R2APBS1_RS16135
hisQ L-histidine ABC transporter, permease component 2 (HisQ)
hutG N-formiminoglutamate formiminohydrolase R2APBS1_RS02515
hutV L-histidine ABC transporter, ATPase component HutV R2APBS1_RS13010 R2APBS1_RS12060
hutW L-histidine ABC transporter, permease component HutW R2APBS1_RS12065
hutX L-histidine ABC transporter, substrate-binding component HutX
LAT2 L-histidine transporter R2APBS1_RS15540 R2APBS1_RS16720
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) R2APBS1_RS15240 R2APBS1_RS14330
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) R2APBS1_RS15240 R2APBS1_RS12020
permease L-histidine permease R2APBS1_RS05445 R2APBS1_RS12170
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