GapMind for catabolism of small carbon sources

 

Protein 3608246 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_1650 binding-protein-dependent transport systems inner membrane component (RefSeq)

Length: 385 amino acids

Source: Dino 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
D-cellobiose catabolism aglG' hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
D-glucose catabolism aglG' hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
lactose catabolism aglG' hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
D-maltose catabolism aglG hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
D-maltose catabolism aglG' hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
sucrose catabolism aglG hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
sucrose catabolism aglG' hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
trehalose catabolism aglG hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
trehalose catabolism aglG' hi Inner membrane ABC transporter permease protein (characterized, see rationale) 100% 100% 761.9 Membrane bound sugar transport protein, component of The glucosylglycerol uptake transporter (functions in osmoprotection and also transports sucrose and trehalose (Mikkat and Hagemann, 2000) (most similar to 3.A.1.1.8) 52% 271.9
D-cellobiose catabolism SMc04257 lo ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) 36% 70% 138.3 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
D-cellobiose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 36% 79% 133.3 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
D-glucose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 36% 79% 133.3 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
lactose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 36% 79% 133.3 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
D-maltose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 36% 79% 133.3 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
D-mannose catabolism TT_C0326 lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 36% 79% 133.3 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
sucrose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 36% 79% 133.3 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
trehalose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 36% 79% 133.3 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
D-xylose catabolism gtsC lo ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 32% 74% 116.7 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
D-galactose catabolism PfGW456L13_1896 lo ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 31% 74% 115.5 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
D-cellobiose catabolism msdC2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 34% 66% 100.5 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4
D-maltose catabolism malG lo ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized) 33% 71% 94.4 ABC transporter for D-Maltose and D-Trehalose, permease component 2 60% 451.4

Sequence Analysis Tools

View 3608246 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

MDNIAGSKSSLTWAVQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAMFPSEQNL
TLRAADPDDFRMPQGDLFVVKGNLFEDEGISEAEISVWGTSSRDVAAYTAGETADLGDGE
TITVQSNGAYVWSGTDDQISGRGQRVFVTATTPPEFTFANYENMLLDPNNSEGMARAFFN
TLTVTIPATIIPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHNAI
GIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSF
PALASFAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVS
IAVPLLVFFSMQRFLVRGLLAGSVK

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