GapMind for catabolism of small carbon sources

 

Protein WP_012759923.1 in Rhizobium leguminosarum bv. trifolii WSM1325

Annotation: NCBI__GCF_000023185.1:WP_012759923.1

Length: 861 amino acids

Source: GCF_000023185.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
myo-inositol catabolism PS417_11890 hi Inositol transport system ATP-binding protein (characterized) 44% 98% 443.4 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!) 45% 427.6
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 44% 99% 442.2 Inositol transport system ATP-binding protein 44% 443.4
L-rhamnose catabolism rhaT' med 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) 45% 97% 427.6 Inositol transport system ATP-binding protein 44% 443.4
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 44% 96% 418.7 Inositol transport system ATP-binding protein 44% 443.4
D-xylose catabolism xylG med 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) 45% 99% 408.7 Inositol transport system ATP-binding protein 44% 443.4
D-galactose catabolism ytfR med galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 42% 99% 367.9 Inositol transport system ATP-binding protein 44% 443.4
L-rhamnose catabolism rhaP med RhaP, 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) 36% 92% 203
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 37% 100% 359.4 Inositol transport system ATP-binding protein 44% 443.4
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 38% 96% 359 Inositol transport system ATP-binding protein 44% 443.4
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 38% 96% 359 Inositol transport system ATP-binding protein 44% 443.4
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 39% 98% 357.5 Inositol transport system ATP-binding protein 44% 443.4
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 38% 93% 306.6 Inositol transport system ATP-binding protein 44% 443.4
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 38% 93% 306.6 Inositol transport system ATP-binding protein 44% 443.4

Sequence Analysis Tools

View WP_012759923.1 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

MLDVSGRPKAAGTSATGQVVASLEGVTKFFGGTVAVANVSIELRAGEVLALLGENGAGKS
TCVKLLAGVHRPDGGQVVMLGKPVAFASPLEAQRAGVAVMHQHPGLFPDLSIAENLFIGQ
TGLRWKLDHRQMQSEAARLLTLVGLDVDVTAPLGRLRTSEQQLVEIARALSLDARVLIMD
EPTAALSQREVERLFTVVDNLRPQGVAMMFVGHRMDEIYRVADRIAVLRDGRHVGTEIAA
DLSRERAVQMMVGRSLDGLYPRNNTAPGDVVLDVRGLSCDGSFQDVSFQLRAGEILGFGG
LVGSGRTEIARVLFGIDQPTGGTIAIDGKTMRFASPKDAMGNGIAYVSEDRIGQSLVMDF
PILNNASLTVLDKATRGGLMSREKEIGIAKPFLDRLRLRFKSFDQPVGALSGGNQQKVVL
AKWLATNPRILILDEPTQGIDVQTKADVHAMMTDLAAKGMAIILISSELPELLGMADRMI
VLREGSVTAEFRHDEASQEKVIGAATDAIVKKVDGEIVAKPVPHQDEKSEIPERAAQGTW
RRVLARRELGLFAAIAAVVIPISILNIRMLSGANLSALAMDAGLLMIVAVAQMLVVITRS
IDLSVAAIIGLAAYGAASTIHLHPEIGVMGGVALACVIGLAAGFLNGLIVTYGRVPAIVV
TLGTMSIFRGINSLWAGGTQVSADQVPQAWLDMTAANIFGVPAVLLIAIATLLVVAYILR
NTSIGRELFAIGSNPGGASLIGIPSRARILMAFSAAGLLAGFDGALWASRYATVDARVAY
GFELTVIAAVVVGGIAVRGGSGTVLGVAAGALMLLIINNGLTLVRVDPLWLQGVYGLVIL
AAIGIDALVARRAAGKRKGAH

This GapMind analysis is from Apr 09 2024. 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