GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_1711 in Pseudomonas fluorescens FW300-N1B4

Annotation: ABC-type polar amino acid transport system, ATPase component

Length: 260 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 52% 99% 260 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 52% 100% 256.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 52% 100% 256.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 54% 98% 253.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 252.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 252.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 252.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-histidine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 252.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 252.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 52% 93% 252.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 51% 96% 249.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 53% 90% 248.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 53% 90% 248.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 51% 93% 248.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 51% 93% 248.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 50% 99% 234.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 50% 99% 234.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 98% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 98% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9

Sequence Analysis Tools

View Pf1N1B4_1711 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

MSALIEFKGFNKFFGEQQVLDGIDLQVKPGEVIVILGPSGCGKSTLLRCLNGLEVAHSGS
LNFAGRELLDKGTDWREVRQQIGMVFQSYHLFPHMSVLDNLLLGPLKVQKRERREARAQA
EALLERVGLLDKREAFPRQLSGGQQQRIAIVRSLCMNPKVMLFDEVTAALDPEMVKEVLE
VIQGLAREGMTLLIVTHEMAFARAVADRIVFMDAGRILEQHPPEIFFTNPQTARAQQFLE
KFSYVAALPKTTQTKELELS

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