GapMind for catabolism of small carbon sources

 

Protein Ga0059261_2556 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_2556 ABC-type multidrug transport system, ATPase component

Length: 587 amino acids

Source: Korea in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 56% 127.1 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 95% 113.6 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 95% 113.6 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 95% 113.6 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 34% 54% 110.9 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 32% 86% 102.8 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-arginine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 96% 100.1 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-glutamate catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 96% 100.1 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-histidine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 96% 100.1 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 81% 94.4 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-leucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 81% 94.4 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 81% 94.4 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 81% 94.4 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 81% 94.4 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 81% 94.4 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 31% 60% 82 Probable multidrug ABC transporter ATP-binding protein YbhF 63% 692.2

Sequence Analysis Tools

View Ga0059261_2556 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

MTDLQNAIVFENLFRCFGKNDEVVAIDDLSASIKTGIITGLVGPDGAGKTTLIRMIAGLL
TPTRGKLTVNDLEPASQGDALRQQLGYMPQRFGLYEDLTVLENLTLYSDLRGVDPAKRAD
MFERMLEFTDLKRFTERRAGKLSGGMKQKLGLACTLLGDPQVLLLDEPSVGVDPISRREL
WKMVGDLAGEGKTIIWSTAYLDEAERCPEVILLDHGKPLYCGSPDELAERMQGRSRLIRN
ITGNRRQVLKHALKSDKVQDGVIQGRAVRVVLKDRNDPLDLAEAEAGDGATLEEVKPRLE
DAVIDLLGGGPGGESVVAKLLQDAGQREEAAGEVVIEAKHLTKRFGDFAATDDVSFDVKR
GEIYGLLGPNGAGKSTTFKMLCGLLVPSSGDANVLGYSLKRSPGDARQRLGYMAQKFSLY
GTLSVRQNMEFFAGIYGLDGSDRRERIDAMIDAFALKPYLAMSPDALPLGFKQRLALACA
IMHDPAILFLDEPTSGVDPLTRREFWTHINGVVEKGVTVMVTTHFMDEAEYCDRIGLIYR
GKLIASGAPDDLRAEAATEDDDDPSMEDAFIELVERADRADDERQAA

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