GapMind for catabolism of small carbon sources

 

Protein 3607448 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_0861 inner-membrane translocator (RefSeq)

Length: 305 amino acids

Source: Dino in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism AZOBR_RS08235 lo L-proline and D-alanine ABC transporter, permease component 1 (characterized) 33% 97% 147.9 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-proline catabolism AZOBR_RS08235 lo L-proline and D-alanine ABC transporter, permease component 1 (characterized) 33% 97% 147.9 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-isoleucine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 98% 144.8 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-leucine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 98% 144.8 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-valine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 98% 144.8 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-proline catabolism HSERO_RS00885 lo ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) 30% 97% 137.5 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-arginine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 97% 136.3 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-glutamate catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 97% 136.3 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-histidine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 97% 136.3 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-phenylalanine catabolism livH lo ABC transporter permease (characterized, see rationale) 30% 97% 133.7 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-serine catabolism Ac3H11_1695 lo ABC transporter permease (characterized, see rationale) 30% 97% 133.7 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6
L-tyrosine catabolism Ac3H11_1695 lo ABC transporter permease (characterized, see rationale) 30% 97% 133.7 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 34% 160.6

Sequence Analysis Tools

View 3607448 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSAILLIEQVLNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGSLYMVGAFAAAAVAGATG
SFVLGLAAALAAAAAAGALIEVTIIRRLYARDHLDQVLATFALILIFSEGTRWIFGSFPL
FLEVPAALSGPVTLPFGIEYPAYRLAIIGIGLAIAAALFWLIAKTRIGVQIRAGEADREM
IAALGVDIDRLYTLVFALGAALAGLAGALVGALQSVQVGMGEPVLILAFVVIVIGGIGSI
KGAFVGALLLGLTDTLGRTLLPVAFGTVLEPSMATAVGSALASMAIYILMAGVLIFRPSG
LFGQS

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, the preprint on GapMind for carbon sources, 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