GapMind for catabolism of small carbon sources

 

Protein 6937298 in Shewanella amazonensis SB2B

Annotation: FitnessBrowser__SB2B:6937298

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

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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:

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