Protein CA265_RS04175 in Pedobacter sp. GW460-11-11-14-LB5
Annotation: FitnessBrowser__Pedo557:CA265_RS04175
Length: 232 amino acids
Source: Pedo557 in FitnessBrowser
Candidate for 32 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 39% | 90% | 152.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 38% | 86% | 146.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 38% | 84% | 146.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 37% | 84% | 145.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 37% | 84% | 145.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 84% | 144.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 83% | 143.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 83% | 143.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 85% | 142.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 62% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 62% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 62% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 62% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 62% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 62% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 62% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 62% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 60% | 137.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 60% | 137.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 60% | 137.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 60% | 137.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 37% | 58% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-arginine catabolism | artP | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 90% | 131 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 90% | 131 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 35% | 63% | 119 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 72% | 118.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 31% | 85% | 105.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 59% | 91.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 44% | 203.8 |
Sequence Analysis Tools
View CA265_RS04175 at FitnessBrowser
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
MIKIENLEKVYKTEEVETTALNGINLHVAAGEFVSIMGPSGCGKSTLLNVMGLLDKPENG
SYKFIDTELLTLNDRERSNFRKRNMGFVFQNFNLIDELTVFENIELPLIYNKIPAGERKK
LVNEIIERMNIVNRSGHFPQQLSGGQQQRVAVARALVTKPKLVLADEPTGNLDSSHGNEV
MELLCELNETGTTIVMVTHSSHDASFSNRIINLKDGHVISEKINKSRNEELI
This GapMind analysis is from Sep 17 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