GapMind for catabolism of small carbon sources

 

Protein WP_004120376.1 in Rhizobium freirei PRF 81

Annotation: NCBI__GCF_000359745.1:WP_004120376.1

Length: 626 amino acids

Source: GCF_000359745.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livG med ABC transporter ATP-binding protein (characterized, see rationale) 51% 95% 219.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-leucine catabolism livG med ABC transporter ATP-binding protein (characterized, see rationale) 51% 95% 219.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-phenylalanine catabolism livG med ABC transporter ATP-binding protein (characterized, see rationale) 51% 95% 219.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-proline catabolism HSERO_RS00895 med ABC transporter ATP-binding protein (characterized, see rationale) 51% 95% 219.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-serine catabolism Ac3H11_1693 med ABC transporter ATP-binding protein (characterized, see rationale) 51% 95% 219.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-tyrosine catabolism Ac3H11_1693 med ABC transporter ATP-binding protein (characterized, see rationale) 51% 95% 219.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-alanine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 42% 98% 212.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-serine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 42% 98% 212.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-threonine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 42% 98% 212.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-valine catabolism livG med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 42% 98% 212.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
D-alanine catabolism AZOBR_RS08245 med Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 42% 96% 203 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-proline catabolism AZOBR_RS08245 med Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 42% 96% 203 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-arginine catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 43% 92% 198 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-glutamate catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 43% 92% 198 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-histidine catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 43% 92% 198 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-isoleucine catabolism natA med NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 41% 96% 175.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-leucine catabolism natA med NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 41% 96% 175.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-proline catabolism natA med NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 41% 96% 175.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-valine catabolism natA med NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 41% 96% 175.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 95% 169.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 39% 98% 169.5 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 34% 276.6

Sequence Analysis Tools

View WP_004120376.1 at NCBI

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

MVRIRRGTVVGIVATVLPLVIATLVAAGLFPGGGERLVTLFLIYVVAVIGTSVYSGNSGI
ISFGNTGFMAIGAYAAGLLTISPIIQKTALPHLPVWLTGWGLPFIPALLVALVVVALVAI
AIGIPVARLAGSSASICTLGFLVIVHVVLVASSDFTRGSQTFFGIPRAVNIWMALPFAIV
AVAIARIYRDSSAGMKLRASREDEIASTAVGVNVRLHRFLAWVLGAVLSGAAGVLLGHFI
GAFSPKDFYFNLTFLLLAMLILGGITTVSGAVIGTAVIMVIVELLRKLEGGVDLGFFSLP
TVFGLTDIGIGLAILLVMYRLQDGLLGVREIDEQLPLLKRLAGGKAHSAAKPATTEAASI
EGDVLRVENVGKRFSGLVALEDANFEVRPGLVTGLIGPNGAGKSTLINSISGVVPPSTGR
VTVGGVDVASLPVHRVPIAGLARTFQNIRLFKNLTALENVTVAASAIARDGADPVDLARE
ALFEVGLGDVADQLAGTLSYGAQRRLEIARALALKPRYLLLDEPAAGMNPAETMELMAVL
DRIRTKYRLGLLVVEHDLKLIMRLCDIVVVLNKGQQIAIGTPAEIQSNPAVIEAYIGRRR
SVAKHEPSKTEAPLLNLDPHTSGKTA

This GapMind analysis is from Sep 24 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