Protein WP_075384684.1 in Alkalihalobacterium alkalinitrilicum DSM 22532
Annotation: NCBI__GCF_002019605.1:WP_075384684.1
Length: 405 amino acids
Source: GCF_002019605.1 in NCBI
Candidate for 12 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | opuBA | med | 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) | 58% | 95% | 448.4 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| L-proline catabolism | proV | med | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 50% | 99% | 374.8 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 62% | 96% | 334 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 57% | 96% | 302 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 32% | 91% | 173.3 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| trehalose catabolism | thuK | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 32% | 91% | 173.3 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 38% | 60% | 167.9 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 37% | 63% | 162.5 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 67% | 161.8 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 31% | 86% | 159.1 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 37% | 63% | 154.8 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 30% | 69% | 124 | Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 | 71% | 560.8 |
Sequence Analysis Tools
View WP_075384684.1 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
MSKIKVEGLTKIFGKKPKRALDMLKQQKSKDEILKETNMTVGVNRASFEVSHGEIFVIMG
LSGSGKSTLVRLLNRLIEPTDGSVWIDGEDLAQMDERKLREVRRSKMSMVFQKFGLFPFR
TIIENVEYGLEVQGILKQERRIQAQTSLELVGLKGYEDKYPNELSGGMQQRVGLARALAN
DPDVLLMDEAFSALDPLIRKDMQDELLDLQEQMKKTIIFITHDLDEALRIGDRIMIMKDG
AIIQVGTPEEILTNPENEYVERFVEDVDRSKVFTAQHVMMRPETVNLEKDGPRVALQRMK
EAGISSIFVTKRNKELLGIVHADKVSKLVKENNNSLLDIIEENVPQVNSDTPLNELMDMA
STSPVPIAVVDEQKLKGIIIRGAVLAALSGSEVNFNGPITEASIS
This GapMind analysis is from Apr 09 2024. 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