GapMind for catabolism of small carbon sources

 

Protein RR42_RS01585 in Cupriavidus basilensis 4G11

Annotation: FitnessBrowser__Cup4G11:RR42_RS01585

Length: 464 amino acids

Source: Cup4G11 in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism N515DRAFT_2924 med Basic amino acid/polyamine antiporter, APA family (characterized, see rationale) 47% 99% 418.3 Uncharacterized amino acid permease YhdG 68% 634.0
L-histidine catabolism Ga0059261_1577 med L-glutamine and L-histidine transporter (characterized) 44% 99% 374 Uncharacterized amino acid permease YhdG 68% 634.0
L-proline catabolism CCNA_00435 med Amino acid transporter (characterized, see rationale) 42% 96% 350.5 Uncharacterized amino acid permease YhdG 68% 634.0
L-isoleucine catabolism bcaP lo Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized) 36% 99% 295.8 Uncharacterized amino acid permease YhdG 68% 634.0
L-leucine catabolism bcaP lo Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized) 36% 99% 295.8 Uncharacterized amino acid permease YhdG 68% 634.0
L-valine catabolism bcaP lo Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized) 36% 99% 295.8 Uncharacterized amino acid permease YhdG 68% 634.0
L-arginine catabolism CAT1 lo high affinity cationic amino acid transporter 1 (characterized) 34% 68% 257.3 Uncharacterized amino acid permease YhdG 68% 634.0
L-lysine catabolism Slc7a1 lo high affinity cationic amino acid transporter 1 (characterized) 34% 68% 257.3 Uncharacterized amino acid permease YhdG 68% 634.0
L-tyrosine catabolism CAT lo Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized) 34% 73% 244.6 Uncharacterized amino acid permease YhdG 68% 634.0

Sequence Analysis Tools

View RR42_RS01585 at FitnessBrowser

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

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Sequence

MSLFRTKNIEAMLAAARDDGLKKVLGPVDLILMGIGAIIGTGIFVLTGTGALTAGPALTV
SFVIAALACGFAALCYAEFASAIPVSGSIYTYSYATLGEIVAWMIGWDLLLEYGLATSAV
SVGWSGYFQSLMAGFGIHLPAMLTAAPGAVPGVQTLFNLPAAVIMLLITWVVSYGVRESA
RLNNVMVAVKIAVVLLFIGVGVWHVKPANWHPFAPFGLDGVFNAAALVFFAFIGFDAVTS
AAEEVRNPRRDLPIGIIGSLAVCTVLYVTVAAIMTGIVPFAKFAGIDHPVSLALQYAGEN
WVAGFVDLGAILGMTTVILVMTFGQTRIIFAMSRDGLLPERLSTVHPVHATPFFATWTVG
IVFAFIAAFVPLNVLAELINIGTLSAFTLISVAVLVLRKTRPDLPRAFRCPGVPVVPLLS
VGFCLFLMAHLQALTWVAFLAWLAIGLAIYFLYARRNAVLHGGA

This GapMind analysis is from Sep 17 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:

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:

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