GapMind for catabolism of small carbon sources

 

L-histidine catabolism in Nocardioides dokdonensis FR1436

Best path

natA, natB, natC, natD, natE, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-histidine ABC transporter, ATPase component 1 (NatA) I601_RS18175 I601_RS02125
natB L-histidine ABC transporter, substrate-binding component NatB I601_RS18165
natC L-histidine ABC transporter, permease component 1 (NatC) I601_RS18180
natD L-histidine ABC transporter, permease component 2 (NatD) I601_RS18185 I601_RS10450
natE L-histidine ABC transporter, ATPase component 2 (NatE) I601_RS18170 I601_RS10465
hutH histidine ammonia-lyase I601_RS03120
hutU urocanase I601_RS03115
hutI imidazole-5-propionate hydrolase I601_RS04775
hutF N-formiminoglutamate deiminase I601_RS04780
hutG' N-formylglutamate amidohydrolase
Alternative steps:
aapJ L-histidine ABC transporter, substrate-binding component AapJ
aapM L-histidine ABC transporter, permease component 2 (AapM) I601_RS07010 I601_RS09275
aapP L-histidine ABC transporter, ATPase component AapP I601_RS09290 I601_RS07015
aapQ L-histidine ABC transporter, permease component 1 (AapQ) I601_RS07010
Ac3H11_2554 ABC transporter for L-Histidine, permease component 2 I601_RS09280 I601_RS08985
Ac3H11_2555 L-histidine ABC transporter, substrate-binding component 2
Ac3H11_2560 L-histidine ABC transporter, ATPase component I601_RS08935 I601_RS02540
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 I601_RS07015 I601_RS09290
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 I601_RS07010
BPHYT_RS24010 L-histidine ABC transporter, permease component 2 I601_RS07010
BPHYT_RS24015 L-histidine ABC transporter, ATPase component I601_RS07015 I601_RS09290
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) I601_RS10450 I601_RS02135
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) I601_RS19350 I601_RS05910
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) I601_RS05900 I601_RS10465
Ga0059261_1577 L-histidine transporter
hisJ L-histidine ABC transporter, substrate-binding component HisJ
hisM L-histidine ABC transporter, permease component 1 (HisM) I601_RS09275 I601_RS07010
hisP L-histidine ABC transporter, ATPase component HisP I601_RS07015 I601_RS08990
hisQ L-histidine ABC transporter, permease component 2 (HisQ) I601_RS05610
hutG N-formiminoglutamate formiminohydrolase
hutV L-histidine ABC transporter, ATPase component HutV I601_RS12915 I601_RS08290
hutW L-histidine ABC transporter, permease component HutW I601_RS12920 I601_RS02545
hutX L-histidine ABC transporter, substrate-binding component HutX
LAT2 L-histidine transporter
LHT L-histidine transporter
PA5503 L-histidine ABC transporter, ATPase component I601_RS01500 I601_RS07015
PA5504 L-histidine ABC transporter, permease component I601_RS01505
PA5505 L-histidine ABC transporter, substrate-binding component I601_RS01495
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