Protein WP_089221336.1 in Sphingomonas laterariae LNB2
Annotation: NCBI__GCF_900188165.1:WP_089221336.1
Length: 271 amino acids
Source: GCF_900188165.1 in NCBI
Candidate for 20 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 41% | 80% | 157.5 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 57% | 141 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 33% | 73% | 140.6 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| L-arginine catabolism | artP | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 37% | 87% | 136.7 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 37% | 87% | 136.7 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 36% | 55% | 132.9 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 33% | 62% | 131.7 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 37% | 53% | 130.2 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 33% | 60% | 129.8 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 32% | 56% | 129.8 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 34% | 54% | 124.8 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 98% | 112.1 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 98% | 112.1 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 98% | 112.1 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 98% | 112.1 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| D-lactate catabolism | PGA1_c12640 | lo | D-lactate transporter, ATP-binding component (characterized) | 32% | 87% | 107.8 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| L-isoleucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 88% | 105.5 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| L-leucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 88% | 105.5 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 88% | 105.5 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
| L-valine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 88% | 105.5 | CynD, component of Bispecific cyanate/nitrite transporter | 46% | 167.5 |
Sequence Analysis Tools
View WP_089221336.1 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
MSALLSLHDVWVEYGDKIVLERVSLDIAARSFVSVVGPSGAGKSTFLRLILGQEAPTRGE
VLLDGKPLRRECDADRGVVFQRYSVFPHLTALQNVMFGRECEQAPVTGRLFGSRRRAAIA
EAEAMLEAVGLEHSRHVYPAQMSGGMQQRLAIAQALIKHPRILLLDEPFGALDPGIRLDM
HALVTRLWRERGLTIVMVTHDIREAFKLSTRVLAFDKRRHDPHAPHRFGSTATYDVPLDR
KADDAAGTVADQPGPAIAPATALSLSNEEAE
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