GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Oceanisphaera arctica V1-41

Best path

aapJ, aapQ, aapM, aapP, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ L-histidine ABC transporter, substrate-binding component AapJ UN63_RS01075
aapQ L-histidine ABC transporter, permease component 1 (AapQ) UN63_RS01070 UN63_RS12585
aapM L-histidine ABC transporter, permease component 2 (AapM) UN63_RS01065 UN63_RS13375
aapP L-histidine ABC transporter, ATPase component AapP UN63_RS01060 UN63_RS12580
hutH histidine ammonia-lyase UN63_RS08680
hutU urocanase UN63_RS08685
hutI imidazole-5-propionate hydrolase UN63_RS08695
hutG N-formiminoglutamate formiminohydrolase UN63_RS08690 UN63_RS13705
Alternative steps:
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 UN63_RS12585 UN63_RS04695
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 UN63_RS12590 UN63_RS13380
Ac3H11_2560 L-histidine ABC transporter, ATPase component UN63_RS03975 UN63_RS02300
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 UN63_RS03190 UN63_RS12580
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component UN63_RS03185 UN63_RS02825
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 UN63_RS03180 UN63_RS13375
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 UN63_RS03175 UN63_RS13370
BPHYT_RS24015 L-histidine ABC transporter, ATPase component UN63_RS03190 UN63_RS12580
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC UN63_RS11720
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) UN63_RS11725
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) UN63_RS11730
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) UN63_RS11735 UN63_RS11740
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) UN63_RS11740 UN63_RS06410
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ UN63_RS02420 UN63_RS03185
hisM L-histidine ABC transporter, permease component 1 (HisM) UN63_RS03175 UN63_RS13370
hisP L-histidine ABC transporter, ATPase component HisP UN63_RS03190 UN63_RS12580
hisQ L-histidine ABC transporter, permease component 2 (HisQ) UN63_RS03180 UN63_RS13375
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV UN63_RS04530 UN63_RS02300
hutW L-histidine ABC transporter, permease component HutW UN63_RS04535 UN63_RS04525
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) UN63_RS11735 UN63_RS06410
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) UN63_RS11725
natE L-histidine ABC transporter, ATPase component 2 (NatE) UN63_RS11740 UN63_RS01085
PA5503 L-histidine ABC transporter, ATPase component UN63_RS12060 UN63_RS12580
PA5504 L-histidine ABC transporter, permease component UN63_RS12065
PA5505 L-histidine ABC transporter, substrate-binding component UN63_RS12070 UN63_RS04020
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