GapMind for catabolism of small carbon sources

 

Protein WP_110805317.1 in Rhodobacter viridis JA737

Annotation: NCBI__GCF_003217355.1:WP_110805317.1

Length: 505 amino acids

Source: GCF_003217355.1 in NCBI

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2'-deoxyinosine catabolism nupA lo Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) 37% 98% 337 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
D-galactose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 97% 300.8 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
L-fucose catabolism HSERO_RS05250 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 35% 93% 297.4 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
D-xylose catabolism xylG lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 34% 99% 295.4 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
D-ribose catabolism rbsA lo ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 35% 98% 295 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
myo-inositol catabolism iatA lo Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 36% 98% 287.3 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 34% 94% 286.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
L-rhamnose catabolism rhaT' lo RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 35% 92% 277.7 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 33% 95% 264.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 33% 93% 256.5 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 38% 339.7

Sequence Analysis Tools

View WP_110805317.1 at NCBI

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

Fitness BLAST: loading...

Sequence

MTGSLLKIEGLTKAYPGVVANDGVGFEVAPGEVHALLGENGAGKSTLVKMIYGLVKPDAG
RMTFQGRPYTPAEPRAARAAGVAMVFQHFSLFEALNVAENVALGMENPPPMGDLAERIRA
ISTAYGLPLDPARTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFHTL
RKLAAEGTAILYISHKLEEIRSLCDGATILRGGKVVASCIPREKSARELAELMVGGEFAA
TDRAGRVSGATILEVDHLNLPPMTQFGPALKNVSFSLAAGEVLGIGGVAGNGQEELLATL
SGERPSGAGTVSLHGQDISDLGPNDRRRLGLLAAPEERLGHAAVPNLSLTENAILTGTVR
RPLTRNGFLNMGAARRFAEEIIKGFDVRTPGPHVAARALSGGNLQKFVIGREVLQSPEVL
VVNQPTWGVDAAAAAAIRQSLLDLAAKGAAVIVISQDLDELMEIADRFCALNEGRLSEPR
PTEGLTMEEIGLMLGGAHGMQEAAL

This GapMind analysis is from Sep 24 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