Protein WP_152617803.1 in Streptacidiphilus oryzae TH49
Annotation: NCBI__GCF_000744815.1:WP_152617803.1
Length: 355 amino acids
Source: GCF_000744815.1 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 |
|---|
| D-cellobiose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, 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) | 35% | 98% | 199.5 | Ribose import permease protein RbsC | 33% | 181.4 |
| D-glucose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, 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) | 35% | 98% | 199.5 | Ribose import permease protein RbsC | 33% | 181.4 |
| lactose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, 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) | 35% | 98% | 199.5 | Ribose import permease protein RbsC | 33% | 181.4 |
| D-maltose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, 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) | 35% | 98% | 199.5 | Ribose import permease protein RbsC | 33% | 181.4 |
| sucrose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, 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) | 35% | 98% | 199.5 | Ribose import permease protein RbsC | 33% | 181.4 |
| trehalose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, 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) | 35% | 98% | 199.5 | Ribose import permease protein RbsC | 33% | 181.4 |
| D-xylose catabolism | xylH | med | Putative beta-xyloside ABC transporter, permease component, 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) | 35% | 98% | 199.5 | Ribose import permease protein RbsC | 33% | 181.4 |
| D-fructose catabolism | frcC | lo | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 35% | 96% | 179.1 | Putative beta-xyloside ABC transporter, permease component, 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 | 35% | 199.5 |
| L-rhamnose catabolism | rhaP | lo | 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) | 34% | 96% | 179.1 | Putative beta-xyloside ABC transporter, permease component, 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 | 35% | 199.5 |
| sucrose catabolism | frcC | lo | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 35% | 96% | 179.1 | Putative beta-xyloside ABC transporter, permease component, 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 | 35% | 199.5 |
| D-mannose catabolism | HSERO_RS03645 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 33% | 96% | 174.9 | Putative beta-xyloside ABC transporter, permease component, 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 | 35% | 199.5 |
| D-galactose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 32% | 96% | 169.9 | Putative beta-xyloside ABC transporter, permease component, 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 | 35% | 199.5 |
| 2'-deoxyinosine catabolism | H281DRAFT_01112 | lo | deoxynucleoside transporter, permease component 2 (characterized) | 34% | 88% | 144.4 | Putative beta-xyloside ABC transporter, permease component, 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 | 35% | 199.5 |
Sequence Analysis Tools
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Sequence
MTSMTEPAQQGQGRDRASTAAGGGRTGLLDWVLKVRELAIAAVLVLMLGATQLANGDFLS
VQGVKDLLLNAAILVLVATGQAMVVITRNVDLSVGSVLGITAFAAGDFLQGGGDPVLGVV
IAVAVGAGFGAVNGLLVSIGRVPALVVTLGTLYIIRGLDSIWVGSREITANQLPSGFSEF
GHSGLSAIPYLGVLAAVVLAAVAYYLRSYRSGRELYAMGSNQEAALLVGVPVRKRLLAAY
VACGALAGLAGALYLARFGNVDSGTGSGYELTVVSAVVVGGVAFTGGSGSVYGAALGAVL
LTSINSVLPAIGVSSVWVLAIDGVMLLLAIAVDRLVALRVARILRERAAQTRSGR
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