Protein WP_039105694.1 in Frischella perrara PEB0191
Annotation: NCBI__GCF_000807275.1:WP_039105694.1
Length: 334 amino acids
Source: GCF_000807275.1 in NCBI
Candidate for 9 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-mannose catabolism | TM1749 | med | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 42% | 98% | 238.8 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
| 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) | 34% | 94% | 181 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 86% | 167.5 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 84.3 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 84.3 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 84.3 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 84.3 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 84.3 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 84.3 | SapD protein, component of Peptide transporter, SapABCDF. Mutants are more sensitive than the wild type to wheat alpha-thionin and to snakin-1, which is the most abundant antimicrobial peptide from potato tubers. They were also less virulent than was the wild-type strain in potato tubers: lesion areas were 37% that of the control, and the growth rate was two orders of magnitude lower. Thus, the interaction of antimicrobial peptides from the host with the sapA-F operon from the pathogen plays a similar role in animal and in plant bacterial pathogenesis | 72% | 501.5 |
Sequence Analysis Tools
View WP_039105694.1 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
MALLDIRNLTIEFITPKGLLRAVDRVNLKLNEGEIRGLVGESGSGKSLIAKAILGVTNKN
WLITADRFHFNGIDLLKLSEKQRRKVISANISMIFQEPQSCLDPNMKIGRLLVQSIPSWT
FKGHFWQRLFWRKNRAIELLHRVGIKEHKDIMNSYPYELTEGECQKVMIATALANQPKLL
IADEPTNAMESTTEAQIFRLLASLNQNSGTTILLISHDLQMVTRWTDRINVLYCGQTVEV
ANSEELIKKPYHPYTQALIFAIPDFGKAIAHKSPLNTLAGVIPPLEHLPIGCRLGPRCPY
AQKKCIETPALIALKDHAVACHYPLNIELQDNKP
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