GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Photobacterium gaetbulicola Gung47

Best path

hutV, hutW, hutX, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hutV L-histidine ABC transporter, ATPase component HutV H744_RS02715 H744_RS22590
hutW L-histidine ABC transporter, permease component HutW H744_RS02720 H744_RS22595
hutX L-histidine ABC transporter, substrate-binding component HutX H744_RS02725
hutH histidine ammonia-lyase H744_RS17380 H744_RS07950
hutU urocanase H744_RS17385
hutI imidazole-5-propionate hydrolase H744_RS17395
hutG N-formiminoglutamate formiminohydrolase H744_RS17390 H744_RS21485
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ H744_RS20715 H744_RS06585
aapM L-histidine ABC transporter, permease component 2 (AapM) H744_RS20725 H744_RS06575
aapP L-histidine ABC transporter, ATPase component AapP H744_RS20730 H744_RS06570
aapQ L-histidine ABC transporter, permease component 1 (AapQ) H744_RS20720 H744_RS06580
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 H744_RS04735 H744_RS14480
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 H744_RS20565 H744_RS14470
Ac3H11_2560 L-histidine ABC transporter, ATPase component H744_RS07760 H744_RS19165
Ac3H11_2561 L-histidine ABC transporter, permease component 1 H744_RS07755
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA H744_RS04730 H744_RS14465
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component H744_RS14470
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 H744_RS14475 H744_RS20570
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 H744_RS20575 H744_RS14480
BPHYT_RS24015 L-histidine ABC transporter, ATPase component H744_RS14465 H744_RS20730
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) H744_RS07090
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) H744_RS07085 H744_RS19165
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ H744_RS14470 H744_RS20565
hisM L-histidine ABC transporter, permease component 1 (HisM) H744_RS14480 H744_RS20575
hisP L-histidine ABC transporter, ATPase component HisP H744_RS14465 H744_RS20730
hisQ L-histidine ABC transporter, permease component 2 (HisQ) H744_RS14475 H744_RS20570
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
LAT2 L-histidine transporter
LHT L-histidine transporter
natA L-histidine ABC transporter, ATPase component 1 (NatA) H744_RS07090 H744_RS12065
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) H744_RS07085 H744_RS20505
PA5503 L-histidine ABC transporter, ATPase component H744_RS13535 H744_RS04730
PA5504 L-histidine ABC transporter, permease component H744_RS13530
PA5505 L-histidine ABC transporter, substrate-binding component H744_RS13525
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