Protein WP_048507544.1 in Chryseobacterium angstadtii KM
Annotation: NCBI__GCF_001045465.1:WP_048507544.1
Length: 240 amino acids
Source: GCF_001045465.1 in NCBI
Candidate for 33 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 61% | 147.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 61% | 147.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 61% | 147.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 61% | 147.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 61% | 147.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 61% | 147.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 61% | 147.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 61% | 147.5 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 84% | 144.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 84% | 144.1 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 60% | 143.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 60% | 143.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 60% | 143.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 36% | 60% | 143.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 37% | 90% | 143.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 36% | 75% | 143.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-arginine catabolism | artP | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 34% | 96% | 142.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 34% | 96% | 142.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 34% | 88% | 138.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 34% | 88% | 138.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 61% | 138.7 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 36% | 85% | 138.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 34% | 88% | 134.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 34% | 89% | 132.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 34% | 89% | 132.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 59% | 129.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 59% | 129.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 33% | 83% | 129.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 34% | 78% | 120.6 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| L-proline catabolism | opuBA | lo | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 35% | 66% | 119 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 55% | 106.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| 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) | 31% | 88% | 104.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 31% | 85% | 101.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 212.2 |
Sequence Analysis Tools
View WP_048507544.1 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
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Sequence
MINVQNLSKIYKTEDVQTNALNNISLHIKEGEFVAIMGPSGCGKSTFLNILGLLDDASAG
SYKFAEVETVKAGEKKKSAIRKKNIGFIFQNFNLIDDLTVYENIELPLIYNGVSSSERKR
RVEEIMEQINIGHRARHYPQQLSGGQQQRAAVARALVTKPQLILADEPTGNLDSSNGNEV
MNLLAELHREGSTIVMVTHSSYDAGFASRIVNMKDGEIFNEEHASQRRDVFEKADAQELQ
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