GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_1414 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_1414 ATPase

Length: 241 amino acids

Source: SynE in FitnessBrowser

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-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 92% 159.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-arginine catabolism artP med histidine transport ATP-binding protein hisP (characterized) 40% 96% 153.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-glutamate catabolism gltL med Amino acid ABC transporter ATP binding protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 41% 90% 153.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 40% 96% 153.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 87% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 87% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-asparagine catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 41% 88% 151.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-aspartate catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 41% 88% 151.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 39% 90% 156 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 38% 93% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 86% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 86% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 87% 139.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 38% 86% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-asparagine catabolism aapP lo 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) 38% 89% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-aspartate catabolism aapP lo 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) 38% 89% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-glutamate catabolism aapP lo 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) 38% 89% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-histidine catabolism aapP lo 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) 38% 89% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-leucine catabolism aapP lo 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) 38% 89% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
L-proline catabolism aapP lo 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) 38% 89% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 70% 114 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 60% 259.2

Sequence Analysis Tools

View Synpcc7942_1414 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MAESAPPVIQFEHVSKIYGEGETTVRALDHVDFQVRAGEYCAIMGASGSGKSTAMNLIGC
LDRPTAGRYYLDGTDVADLDDDALAAVRNRKIGFVFQQFHLLPQLSAVENVMLPMIYAGI
SQQERRDRAVAALTQVGLAQRLDNKPNQLSGGQQQRVAIARAIVNQPVLLLADEPTGALD
SQTTEEVLNIFDQLHQRGITIVIVTHEAEVADRAERVIWFRDGQIQRETQNPPRPVLAAT
F

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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