Protein WP_047094545.1 in Erythrobacter marinus HWDM-33
Annotation: NCBI__GCF_001013305.1:WP_047094545.1
Length: 229 amino acids
Source: GCF_001013305.1 in NCBI
Candidate for 44 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 | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 40% | 79% | 136.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 80% | 142.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 80% | 142.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 62% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 62% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 62% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 62% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 62% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 35% | 62% | 137.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| 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) | 33% | 50% | 133.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 56% | 130.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 33% | 58% | 127.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 34% | 60% | 125.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 34% | 60% | 125.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 63% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 63% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 63% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 63% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 63% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 63% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 63% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 63% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 65% | 121.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 65% | 121.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 31% | 51% | 121.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 34% | 56% | 120.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 56% | 119 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 61% | 118.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| 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) | 32% | 68% | 117.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 34% | 57% | 115.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| 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) | 32% | 88% | 114.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 63% | 107.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 33% | 72% | 107.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-cellobiose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 106.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-glucose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 106.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| lactose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 106.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-maltose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 106.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| sucrose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 106.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| trehalose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 33% | 87% | 106.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 32% | 85% | 105.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 32% | 85% | 105.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 32% | 85% | 105.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 32% | 85% | 105.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 56% | 105.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 41% | 184.1 |
Sequence Analysis Tools
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
MSARNISRDFEAGQETIRVLHGIDLDVCPGELTYLVGESGSGKTTLISIMCGILWPTEGS
VEVFGTDIYGLTDDDLVDFRLQNIGFIFQQYNLIPAIDAASNAAVPLIAQGMDRRKARAK
AAEMLDALNIADQADKLPNQLSGGQQQRVAIARALVHEPRLVVCDEPTAALDAKSGRRVM
DLLRDVALAEDRSVIIVTHDNRIFDLADRILVLEDGRITHDGTDVPDDH
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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