GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_1433 in Pseudomonas fluorescens FW300-N2E2

Annotation: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Length: 260 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism HSERO_RS00895 hi ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 43% 100% 208.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-arginine catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 89% 202.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-glutamate catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 89% 202.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-histidine catabolism braF med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 89% 202.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-isoleucine catabolism livG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 89% 202.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-leucine catabolism livG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 89% 202.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-valine catabolism livG med ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 89% 202.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-phenylalanine catabolism livG med ABC transporter ATP-binding protein (characterized, see rationale) 41% 99% 200.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-serine catabolism Ac3H11_1693 med ABC transporter ATP-binding protein (characterized, see rationale) 41% 99% 200.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-tyrosine catabolism Ac3H11_1693 med ABC transporter ATP-binding protein (characterized, see rationale) 41% 99% 200.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
D-alanine catabolism AZOBR_RS08245 med Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 44% 90% 195.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-proline catabolism AZOBR_RS08245 med Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 44% 90% 195.3 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 196.4 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 196.4 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 196.4 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 94% 164.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 94% 164.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 94% 164.9 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
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) 35% 96% 154.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7
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) 35% 96% 154.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 44% 198.7

Sequence Analysis Tools

View Pf6N2E2_1433 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

MTQTAITHLLELDHISLSFKGVKAVTDISFRVAAGEICALIGPNGAGKSSLLNVISGVYQ
AQDGHIRFDRQERRRMRPHDVAVRGIARTFQNIALFKGMSVLDNVLTGRNLKRRSTWIEQ
ALRIGRARTEDDRQREAAERVIAFLHLQPWRDTLVGTLPYGLQKRVELARALAAEPRLLL
LDEPMAGMNADEKQQMSRFIVDINRELGTTVVLIEHDIGVVMDISDHVVVLDYGRKIGDG
SPEDVRQNPEVISAYLGTRH

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