Protein WP_110806538.1 in Rhodobacter viridis JA737
Annotation: NCBI__GCF_003217355.1:WP_110806538.1
Length: 358 amino acids
Source: GCF_003217355.1 in NCBI
Candidate for 5 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
putrescine catabolism | potA | hi | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 50% | 87% | 286.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 273.5 |
D-mannitol catabolism | mtlK | med | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 41% | 93% | 253.8 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 50% | 286.2 |
D-sorbitol (glucitol) catabolism | mtlK | med | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 41% | 93% | 253.8 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 50% | 286.2 |
D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 39% | 96% | 241.5 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 50% | 286.2 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 39% | 95% | 162.9 | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 | 50% | 286.2 |
Sequence Analysis Tools
View WP_110806538.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
Sequence
MSRSRLLDIRAARRLFTTPEGKSFAALDGVDLAVDEGEFVTLLGPSGCGKTTLLRAIAGF
EELDEGVIRLDGADLSGLPPHRRPVNTVFQSYALFPHMSVARNVGYALEVQGAPRAEREA
EVAAALEKVGLAGLGTRRPAQLSGGQRQRVALARAIVAKPRLLLLDEPLSALDRNLRQQM
QFELKDLQHRLGIAFVFVTHDQEEALTMSDRIVVLRAGKVEQAAPPREIYRHPKTRFVAE
FIGETNLLPARVEGISGAQALLSLPGGQSLQAEAAGLEPGRTVTAVLRPTDITLGTGDLA
GTLLRADFMGADRHLRVALEGGPEISVIARDTAVLPQPGTRLHLGCDPALVHVMEEPT
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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