Protein WP_047007739.1 in Erythrobacter gangjinensis K7-2
Annotation: NCBI__GCF_001010925.1:WP_047007739.1
Length: 239 amino acids
Source: GCF_001010925.1 in NCBI
Candidate for 29 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 38% | 88% | 146.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 34% | 50% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 85% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 85% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
L-glutamate catabolism | gltL | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 85% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 63% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 33% | 88% | 121.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 36% | 64% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 67% | 118.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 33% | 58% | 109.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-cellobiose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-glucose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
lactose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-maltose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
sucrose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
trehalose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 85% | 101.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 56% | 101.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 85% | 101.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 85% | 101.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 85% | 101.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 31% | 62% | 101.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 182.6 |
Sequence Analysis Tools
View WP_047007739.1 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
MSPTPDNNAAISVRGITRDFEAGQQTITVLHGIDTDIRAGELTYVVGESGSGKTTLISIM
CGILWPTEGEVQVFGTDIYSLSDTDLVEFRLNNIGFIFQQYNLIPSIDAASNASVPLIAQ
GMDRDEARERAVAIMDKLNIRDQAGKLPSQLSGGQQQRVAIARALVHEPRLVVCDEPTAA
LDASSGRRVMDLLREVAVAEDRACIIVTHDNRVFDLADRILVLEDGKITHDGKEMPEDH
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