GapMind for catabolism of small carbon sources

 

Protein WP_085545256.1 in Dethiosulfovibrio salsuginis USBA 82

Annotation: NCBI__GCF_900177735.1:WP_085545256.1

Length: 503 amino acids

Source: GCF_900177735.1 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
2'-deoxyinosine catabolism nupA med RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) 45% 98% 436.8 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
D-cellobiose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 94% 325.9 RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases 45% 436.8
D-galactose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 94% 325.9 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
D-glucose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 94% 325.9 RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases 45% 436.8
lactose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 94% 325.9 RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases 45% 436.8
D-maltose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 94% 325.9 RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases 45% 436.8
sucrose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 94% 325.9 RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases 45% 436.8
trehalose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 94% 325.9 RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases 45% 436.8
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) 39% 98% 325.5 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
D-ribose catabolism rbsA lo ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) 39% 94% 318.2 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 36% 91% 307.4 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 35% 98% 292.7 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 36% 91% 289.3 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
D-fructose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 36% 89% 276.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
sucrose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 36% 89% 276.6 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 35% 96% 155.2 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 98% 141 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 98% 141 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 98% 141 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
D-alanine catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 81% 94.7 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4
L-proline catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 81% 94.7 Glucose import ATP-binding protein TsgD13; EC 7.5.2.- 44% 451.4

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Sequence

MKGITKSFQGIKANDQIDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDIGGT
RLSFRSPNDAISAGIGMVHQHFMLVPSQTVWENMVLGLPDLPQILPKGKIISEITAISKQ
YGLEVDPEAIIWQLSIGEQQRVEILKTLYRNAQVLILDEPTAVLTPQEARSLFNTIKRMT
EEGRGIIFISHKLDEVMEISDRVTVLRKGKLIGTVDRENASKEKIAEMMVGKRINLDLDK
KDITPGEVVYSLSQANAISDRGLKALDQVSLELREGQILGLAGVAGNGQTELCQVMAGLR
KMTSGKLILKGKEVTDSSPRELIDGGIRYIPADRKGTGMVSNMDVRENSTLKRYWRRPVA
RGVLIDWKAVLKHALGIVKNFNVDTPSVETPVRNLSGGNIQKLMLGRELSDIPKVLIAMN
PTWGLDVAATRFVREQLLEEREKGAAIFLISEDLDELMSLSDRIAVMYRGKIMGLVEDPN
TFGIERIGMMMAGTRIEQVGGGL

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