GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_1414 in Synechococcus elongatus PCC 7942

Annotation: FitnessBrowser__SynE:Synpcc7942_1414

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

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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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:

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