GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Rhodococcus qingshengii djl-6-2

Best path

permease, 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
permease L-histidine permease C1M55_RS07700 C1M55_RS20600
hutH histidine ammonia-lyase C1M55_RS25900 C1M55_RS25965
hutU urocanase C1M55_RS25920
hutI imidazole-5-propionate hydrolase C1M55_RS25925
hutG N-formiminoglutamate formiminohydrolase C1M55_RS25930 C1M55_RS03260
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) C1M55_RS21980 C1M55_RS16560
aapP L-histidine ABC transporter, ATPase component AapP C1M55_RS13925 C1M55_RS21985
aapQ L-histidine ABC transporter, permease component 1 (AapQ)
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 C1M55_RS21980 C1M55_RS07370
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component C1M55_RS19865 C1M55_RS23420
Ac3H11_2561 L-histidine ABC transporter, permease component 1 C1M55_RS24770
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1
bgtA L-histidine ABC transporter, ATPase component BgtA C1M55_RS16555 C1M55_RS21985
bgtB L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) C1M55_RS30350 C1M55_RS21980
BPHYT_RS24000 L-histidine ABC transporter, substrate-binding component
BPHYT_RS24005 L-histidine ABC transporter, permease component 1 C1M55_RS07370 C1M55_RS30350
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 C1M55_RS13915 C1M55_RS07370
BPHYT_RS24015 L-histidine ABC transporter, ATPase component C1M55_RS13925 C1M55_RS07375
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) C1M55_RS06865
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) C1M55_RS16605 C1M55_RS22585
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) C1M55_RS22600 C1M55_RS08560
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) C1M55_RS06875 C1M55_RS22595
Ga0059261_1577 L-histidine transporter C1M55_RS10990 C1M55_RS20005
hisJ L-histidine ABC transporter, substrate-binding component HisJ
hisM L-histidine ABC transporter, permease component 1 (HisM) C1M55_RS21980 C1M55_RS30350
hisP L-histidine ABC transporter, ATPase component HisP C1M55_RS21985 C1M55_RS16555
hisQ L-histidine ABC transporter, permease component 2 (HisQ) C1M55_RS07370 C1M55_RS16560
hutF N-formiminoglutamate deiminase
hutG' N-formylglutamate amidohydrolase
hutV L-histidine ABC transporter, ATPase component HutV C1M55_RS25960 C1M55_RS20380
hutW L-histidine ABC transporter, permease component HutW C1M55_RS20390 C1M55_RS24910
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) C1M55_RS16610 C1M55_RS06870
natB L-histidine ABC transporter, substrate-binding component NatB C1M55_RS16620
natC L-histidine ABC transporter, permease component 1 (NatC) C1M55_RS16605
natD L-histidine ABC transporter, permease component 2 (NatD) C1M55_RS16600
natE L-histidine ABC transporter, ATPase component 2 (NatE) C1M55_RS16615 C1M55_RS22595
PA5503 L-histidine ABC transporter, ATPase component C1M55_RS25665 C1M55_RS02990
PA5504 L-histidine ABC transporter, permease component C1M55_RS25670
PA5505 L-histidine ABC transporter, substrate-binding component C1M55_RS25660
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.

Links

Downloads

Related tools

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