GapMind for catabolism of small carbon sources

 

Protein Ga0059261_2556 in Sphingomonas koreensis DSMZ 15582

Annotation: FitnessBrowser__Korea:Ga0059261_2556

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

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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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 (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