Annotation: NCBI__GCF_001431535.1:WP_057507731.1
Length: 276 amino acids
Source: GCF_001431535.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 94% | 144.8 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 65% | 352.4 |
L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 33% | 95% | 131.3 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 65% | 352.4 |
L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 34% | 98% | 126.7 | phosphate import ATP-binding protein pstB; EC 3.6.3.27 | 65% | 352.4 |
View WP_057507731.1 at NCBI
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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MNDLSNAVPMQRIVVPASHESLATPAPVKLTARGLDFYYDKFHALKGIDIEVPEKRVTAL IGPSGCGKSTLLRIFNRIYALYPKLEARGEVLLDGENILSPKYPMNRLRSKVGMVFQKPV PFPMTIFENVAYGIRHHEKLSKADMNDRVEHALRQGALWDEVKDKLGQSALGLSGGQQQR LCIARAVALRPDVLLLDEPTSALDPISTSRIEQLVEELKHDYTIVIVTHNMQQAARVSDY TAFMYLGDLIEHDRTEVIFSQPSKQQTEDYITGRFG
This GapMind analysis is from Apr 09 2024. 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