GapMind for catabolism of small carbon sources

 

Protein HSERO_RS08285 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS08285 amino acid ABC transporter ATP-binding protein

Length: 258 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 18 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 hi High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 65% 99% 347.4 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 42% 205.3
L-phenylalanine catabolism livG hi High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 65% 99% 347.4 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 47% 238.4
L-alanine catabolism braF hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 65% 99% 344 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 60% 318.9
L-leucine catabolism livG hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 65% 99% 344 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 42% 205.3
L-serine catabolism braF hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 65% 99% 344 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 60% 318.9
L-threonine catabolism braF hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 65% 99% 344 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 60% 318.9
L-valine catabolism livG hi High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 65% 99% 344 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 42% 205.3
D-alanine catabolism AZOBR_RS08245 med Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 53% 88% 266.2 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-proline catabolism AZOBR_RS08245 med Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 53% 88% 266.2 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-arginine catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 90% 252.3 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-glutamate catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 90% 252.3 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-histidine catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 90% 252.3 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-histidine catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 40% 96% 202.2 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-leucine catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 40% 96% 202.2 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-proline catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 40% 96% 202.2 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-isoleucine catabolism natA lo 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) 39% 96% 198.4 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
L-valine catabolism natA lo 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) 39% 96% 198.4 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 35% 99% 183 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 65% 344.0

Sequence Analysis Tools

View HSERO_RS08285 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

MNASVKTMLEVSNLSMRFGGLLAVDGVSLAVQEREVFAIIGPNGAGKTTVFNCISGFYRP
TSGEIMLDGASIARQPSHQVAQQGLVRTFQNIRLFKSMTVVENLLVAQHQQVNTNLLSGL
LKTPAYRKSEQEALQRAAYWLDQLGLTALANREAGTLSYGLQRRVEIARCMITKPRLLLL
DEPAAGLNPQEKQELSQLIDRLRREHGVAVLLIEHDMSLIMGISDRILVMEHGKPIVTGT
PEQVRSDERVIKAYLGEE

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