Annotation: FitnessBrowser__Caulo:CCNA_01907
Length: 253 amino acids
Source: Caulo in FitnessBrowser
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 41% | 78% | 156.4 | CynD, component of Bispecific cyanate/nitrite transporter | 45% | 179.1 |
D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 64% | 147.9 | CynD, component of Bispecific cyanate/nitrite transporter | 45% | 179.1 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 38% | 56% | 142.1 | CynD, component of Bispecific cyanate/nitrite transporter | 45% | 179.1 |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 33% | 69% | 137.1 | CynD, component of Bispecific cyanate/nitrite transporter | 45% | 179.1 |
View CCNA_01907 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
MALLSFRNVWVEYGDKVVLENVELSIAQGSFVSIVGPSGAGKSTFLRLVIGQEAPTRGAI DLEGRNLRAEPGPDRGVVFQKYSVFPHLSARDNVVFGLDCAGSALRGKLSGAKRRAALEQ ADAMLAAVGLGDSGDLYPAKMSGGMQQRLAIAQALIKKPRILLLDEPFGALDPGVRLDMH ELITSLWRDNGLTIMMVTHDIKEAFKLGTRVLAFDKRRRDPHAPHRYGATAVYDFPLDKP GAVGPEALAGLGQ
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