GapMind for catabolism of small carbon sources

 

Protein WP_038023703.1 in Tatumella morbirosei LMG 23360

Annotation: NCBI__GCF_000757425.2:WP_038023703.1

Length: 506 amino acids

Source: GCF_000757425.2 in NCBI

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-galactose catabolism ytfR hi galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 74% 100% 730.7 Fructose import ATP-binding protein FruK; EC 7.5.2.- 45% 439.1
L-arabinose catabolism araVsh med ABC transporter related (characterized, see rationale) 53% 99% 511.9 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
D-fructose catabolism fruK med Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 45% 99% 439.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
sucrose catabolism fruK med Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 45% 99% 439.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
myo-inositol catabolism iatA med 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) 40% 97% 360.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 41% 91% 353.2 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 41% 91% 353.2 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
D-ribose catabolism rbsA med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 41% 96% 350.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 38% 100% 355.9 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 37% 97% 317 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 35% 95% 289.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 35% 95% 289.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 93% 168.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 93% 168.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 93% 168.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 93% 168.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 93% 168.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 38% 93% 168.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 34% 95% 159.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 34% 95% 159.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 36% 100% 154.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 74% 730.7

Sequence Analysis Tools

View WP_038023703.1 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

MELSQDTGLLTLKNISKRFPGVKALDDVSFSLRKGEIMALLGENGAGKSTLIKVLTGVYT
RDQGSILLNGREINPRSTAQAQESGIGTVYQEVNLLPNMSVADNLFMGREPRRFGLIDRR
TLNRKASELLREYGFELDVTAPLGVFSVAMQQIIAICRAVDLSGQILILDEPTASLDTSE
VEMLFTLMEKLKARGMSLIFVTHFLDQVYRITDRITVLRNGRYVATRDTATLPQLELIKL
MLGRELLSTSLQRQGRTLHSENPVVSFSQYGRKGDIEPFDLAVRPGEIVGLAGLLGSGRT
ETAEVLFGIRRADQGTASIRGASQNIRTPARASRAGIGFCPEDRKTDGIIGAASVRENII
LALQAQRGWLRPLSRHQQTEIAERLIKSLGIRTPDVEQPVELLSGGNQQKVLLSRWLVTR
PQFLILDEPTRGIDIGAHAEIIRLIESLCADGLALLVISSELEELVGYADRVIILRDHRQ
VAEIPLERLSVGTIMTAIADGGGQNG

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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