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.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| LAT2 | L-histidine transporter | CLV36_RS10645 | |
| hutH | histidine ammonia-lyase | CLV36_RS13245 | |
| hutU | urocanase | CLV36_RS13255 | |
| hutI | imidazole-5-propionate hydrolase | CLV36_RS13260 | |
| hutG | N-formiminoglutamate formiminohydrolase | CLV36_RS13250 | CLV36_RS04090 |
| Alternative steps: | |||
| aapJ | L-histidine ABC transporter, substrate-binding component AapJ | ||
| aapM | L-histidine ABC transporter, permease component 2 (AapM) | CLV36_RS12705 | CLV36_RS07905 |
| aapP | L-histidine ABC transporter, ATPase component AapP | CLV36_RS07915 | CLV36_RS03520 |
| aapQ | L-histidine ABC transporter, permease component 1 (AapQ) | CLV36_RS03525 | |
| Ac3H11_2554 | ABC transporter for L-Histidine, permease component 2 | CLV36_RS02980 | CLV36_RS12705 |
| Ac3H11_2555 | L-histidine ABC transporter, substrate-binding component 2 | CLV36_RS03530 | |
| Ac3H11_2560 | L-histidine ABC transporter, ATPase component | CLV36_RS05080 | CLV36_RS16575 |
| 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 | CLV36_RS03520 | CLV36_RS07915 |
| 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 | CLV36_RS02980 | |
| BPHYT_RS24010 | L-histidine ABC transporter, permease component 2 | CLV36_RS12705 | CLV36_RS02980 |
| BPHYT_RS24015 | L-histidine ABC transporter, ATPase component | CLV36_RS12700 | CLV36_RS02985 |
| 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) | CLV36_RS03605 | CLV36_RS05550 |
| braG | ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | CLV36_RS09960 | CLV36_RS04885 |
| Ga0059261_1577 | L-histidine transporter | CLV36_RS00125 | CLV36_RS10095 |
| hisJ | L-histidine ABC transporter, substrate-binding component HisJ | CLV36_RS02975 | CLV36_RS03530 |
| hisM | L-histidine ABC transporter, permease component 1 (HisM) | CLV36_RS03525 | CLV36_RS02980 |
| hisP | L-histidine ABC transporter, ATPase component HisP | CLV36_RS12700 | CLV36_RS07915 |
| hisQ | L-histidine ABC transporter, permease component 2 (HisQ) | CLV36_RS03525 | CLV36_RS12705 |
| hutF | N-formiminoglutamate deiminase | ||
| hutG' | N-formylglutamate amidohydrolase | ||
| hutV | L-histidine ABC transporter, ATPase component HutV | CLV36_RS16575 | CLV36_RS03605 |
| hutW | L-histidine ABC transporter, permease component HutW | CLV36_RS16570 | CLV36_RS03600 |
| hutX | L-histidine ABC transporter, substrate-binding component HutX | ||
| LHT | L-histidine transporter | ||
| natA | L-histidine ABC transporter, ATPase component 1 (NatA) | CLV36_RS02985 | |
| 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) | CLV36_RS03520 | CLV36_RS08790 |
| PA5503 | L-histidine ABC transporter, ATPase component | CLV36_RS03605 | CLV36_RS07915 |
| PA5504 | L-histidine ABC transporter, permease component | CLV36_RS03600 | |
| PA5505 | L-histidine ABC transporter, substrate-binding component | CLV36_RS03595 | |
| permease | L-histidine permease | CLV36_RS15885 | CLV36_RS08665 |
| 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.
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:
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