GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Belnapia rosea CPCC 100156

Best path

braC, braD, braE, braF, braG, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC BLR02_RS12505
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) BLR02_RS12525 BLR02_RS10285
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) BLR02_RS12520 BLR02_RS10290
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) BLR02_RS12515 BLR02_RS03485
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) BLR02_RS12510 BLR02_RS10300
hutH histidine ammonia-lyase BLR02_RS05140
hutU urocanase BLR02_RS05135
hutI imidazole-5-propionate hydrolase BLR02_RS05145
hutF N-formiminoglutamate deiminase BLR02_RS05115
hutG' N-formylglutamate amidohydrolase BLR02_RS08655
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ BLR02_RS24970 BLR02_RS21740
aapM L-histidine ABC transporter, permease component 2 (AapM) BLR02_RS24960 BLR02_RS10415
aapP L-histidine ABC transporter, ATPase component AapP BLR02_RS24955 BLR02_RS10420
aapQ L-histidine ABC transporter, permease component 1 (AapQ) BLR02_RS24965 BLR02_RS10415
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 BLR02_RS02405 BLR02_RS24960
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2 BLR02_RS19480
Ac3H11_2560 L-histidine ABC transporter, ATPase component BLR02_RS09870 BLR02_RS17160
Ac3H11_2561 L-histidine ABC transporter, permease component 1 BLR02_RS09865 BLR02_RS17165
Ac3H11_2562 L-histidine ABC transporter, substrate-binding component 1 BLR02_RS09860
bgtA L-histidine ABC transporter, ATPase component BgtA BLR02_RS10420 BLR02_RS24955
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 BLR02_RS02410 BLR02_RS10415
BPHYT_RS24015 L-histidine ABC transporter, ATPase component BLR02_RS10420 BLR02_RS24955
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ
hisM L-histidine ABC transporter, permease component 1 (HisM) BLR02_RS10410 BLR02_RS19475
hisP L-histidine ABC transporter, ATPase component HisP BLR02_RS02400 BLR02_RS24955
hisQ L-histidine ABC transporter, permease component 2 (HisQ) BLR02_RS02405 BLR02_RS24965
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV BLR02_RS11065 BLR02_RS06615
hutW L-histidine ABC transporter, permease component HutW BLR02_RS11075 BLR02_RS11070
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) BLR02_RS10295 BLR02_RS02515
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) BLR02_RS19370 BLR02_RS10285
natE L-histidine ABC transporter, ATPase component 2 (NatE) BLR02_RS12510 BLR02_RS00885
PA5503 L-histidine ABC transporter, ATPase component BLR02_RS19985 BLR02_RS10420
PA5504 L-histidine ABC transporter, permease component BLR02_RS19980
PA5505 L-histidine ABC transporter, substrate-binding component BLR02_RS19975
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