GapMind for catabolism of small carbon sources

 

Protein 6937298 in Shewanella amazonensis SB2B

Annotation: Sama_1468 putative macrolide efflux ABC transporter, ATP-binding protein (RefSeq)

Length: 230 amino acids

Source: SB2B in FitnessBrowser

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 90% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 90% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 90% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 40% 80% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 40% 80% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 78% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 40% 82% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 45% 63% 173.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 45% 63% 173.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 45% 63% 173.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 45% 63% 173.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 45% 63% 173.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 45% 63% 173.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 91% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 91% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-glutamate catabolism gltL lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 91% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 58% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 35% 52% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 61% 126.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 57% 122.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 78% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 83% 83.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 83% 83.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 83% 83.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 83% 83.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 57% 249.6

Sequence Analysis Tools

View 6937298 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

MISLQALTKSFRMGDAEVQALRGVDIHIRQNEFVAIMGPSGSGKSTLMNIIGCLDRPTSG
NYLLNGSAVGGLSDDALSAVRNREIGFVFQSFHLLPRLSALDNVLLPLRFSETPRGDRQH
AIELLERVGLGQRLDHRPNQLSGGQRQRVAIARALVNRPTLLLADEPTGALDSKTSVEIM
ALFDELHLSGQTIVLVTHEEEVAECAGRIIRMRDGVVQQDKQKPREVSNG

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