Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_323
Length: 283 amino acids
Source: pseudo13_GW456_L13 in FitnessBrowser
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-histidine catabolism | hutW | hi | ABC transporter for L-Histidine, permease component (characterized) | 97% | 100% | 534.6 | Glycine betaine/proline betaine transport system permease protein ProW | 47% | 245.7 |
L-proline catabolism | hutW | med | HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 63% | 99% | 350.9 | ABC transporter for L-Histidine, permease component | 97% | 534.6 |
L-proline catabolism | proW | med | Glycine betaine/proline betaine transport system permease protein ProW (characterized) | 47% | 75% | 245.7 | ABC transporter for L-Histidine, permease component | 97% | 534.6 |
View PfGW456L13_323 at FitnessBrowser
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Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
MFPESFTFSIADWVNGWVDSLVTNYGDVFRSISDTLLWAIVNLEGLLRAAPWWLMLAIVA GVAWHATRKVVTTAVIVGLLFLVGAVGLWDKLMQTLALMMVATIISVLIGIPLGILSARS NRLRSVLMPLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQV DGEVMEAINAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGED VLVGIQTLNVGRGLEAGLAIVILAVVIDRITQAYGRARHEVSK
This GapMind analysis is from Sep 17 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