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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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