GapMind for catabolism of small carbon sources

 

Protein GFF3784 in Pseudomonas stutzeri RCH2

Annotation: Psest_3853 ABC-type branched-chain amino acid transport systems, ATPase component

Length: 266 amino acids

Source: psRCH2 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-alanine catabolism braF med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 97% 173.7 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 37% 169.9
L-histidine catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 97% 173.7 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 37% 169.9
L-leucine catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 97% 173.7 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 37% 169.9
L-proline catabolism natA med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 97% 173.7 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 37% 169.9
L-serine catabolism braF med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 97% 173.7 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 37% 169.9
L-threonine catabolism braF med NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 97% 173.7 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 37% 169.9
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 38% 99% 169.1 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 38% 99% 169.1 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 38% 99% 169.1 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
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) 37% 96% 168.3 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 37% 169.9
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) 37% 96% 168.3 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 37% 169.9
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 36% 98% 162.5 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 37% 96% 160.2 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 37% 96% 160.2 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 37% 96% 160.2 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-arginine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 34% 93% 146 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-glutamate catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 34% 93% 146 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-histidine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 34% 93% 146 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
D-alanine catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 33% 90% 137.9 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7
L-proline catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 33% 90% 137.9 NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 39% 173.7

Sequence Analysis Tools

View GFF3784 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

MSMAAVHPNPTGNAGRDATVMLSARGLRKEFGGFVAVNNVDLDVRHAQVHALIGPNGAGK
TTVFNLLTKFLQPSAGSIRLLDHDITRTDPAKVARMGLVRSFQISAVFPHLTVLDNVRVA
LQRPGGLATQFWLPMRSLNRLNERALQLIESVGLADKRHELAADLSYGRKRVLEIATTLA
LEPKVLLLDEPMAGMGHEDVHVVAEIIREVATQRAVLMVEHNLKVVADLCHQVTVLQRGE
ILTSGDYRTVSQDERVRVAYMGTDDD

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