GapMind for catabolism of small carbon sources

 

Protein Ga0059261_1577 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_1577 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Length: 470 amino acids

Source: Korea in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ga0059261_1577 hi L-glutamine and L-histidine transporter (characterized) 100% 100% 915.6 Uncharacterized amino acid permease YhdG 43% 380.2
L-proline catabolism CCNA_00435 med Amino acid transporter (characterized, see rationale) 59% 99% 530.8 L-glutamine and L-histidine transporter 100% 915.6
L-proline catabolism N515DRAFT_2924 med Basic amino acid/polyamine antiporter, APA family (characterized, see rationale) 41% 98% 355.9 L-glutamine and L-histidine transporter 100% 915.6
L-isoleucine catabolism bcaP lo Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized) 34% 95% 256.5 L-glutamine and L-histidine transporter 100% 915.6
L-leucine catabolism bcaP lo Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized) 34% 95% 256.5 L-glutamine and L-histidine transporter 100% 915.6
L-valine catabolism bcaP lo Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized) 34% 95% 256.5 L-glutamine and L-histidine transporter 100% 915.6
L-arginine catabolism CAT1 lo high affinity cationic amino acid transporter 1 (characterized) 35% 67% 231.1 L-glutamine and L-histidine transporter 100% 915.6
L-lysine catabolism Slc7a1 lo high affinity cationic amino acid transporter 1 (characterized) 35% 67% 231.1 L-glutamine and L-histidine transporter 100% 915.6

Sequence Analysis Tools

View Ga0059261_1577 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MAGGLFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIGVGAGKAGPAV
IMSFVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVS
TVAVGWSGYAAPLLHAWTGMPLELMAGPHANGIVNLPAIFIIAVVAGLLCLGTKESATLN
AALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPDGVERGVMAAAAIIFFAFY
GFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSPEPLALI
LRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKVSKRGSPVR
ITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRMFRTPLWW
LVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAYARPRVSAKGIE

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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