Protein WP_047213382.1 in Pandoraea thiooxydans ATSB16
Annotation: NCBI__GCF_001931675.1:WP_047213382.1
Length: 377 amino acids
Source: GCF_001931675.1 in NCBI
Candidate for 18 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
putrescine catabolism | potA | hi | PotG aka B0855, component of Putrescine porter (characterized) | 52% | 100% | 383.3 | Maltose-transporting ATPase (EC 3.6.3.19) | 41% | 253.1 |
D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 41% | 87% | 253.1 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
D-mannitol catabolism | mtlK | med | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 40% | 94% | 241.9 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 91% | 238.4 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 91% | 238.4 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 91% | 238.4 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 87% | 236.1 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 40% | 87% | 236.1 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 42% | 83% | 233.4 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 86% | 231.5 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 86% | 231.5 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 86% | 231.5 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 86% | 231.5 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 86% | 231.5 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 86% | 231.5 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 41% | 82% | 220.7 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 38% | 87% | 225.7 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
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) | 32% | 77% | 179.1 | PotG aka B0855, component of Putrescine porter | 52% | 383.3 |
Sequence Analysis Tools
View WP_047213382.1 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
MNEPASMPHESRAERAGHFVQMVGVVKKFGETVAVRHVDLSVKKGELFALLGSSGCGKST
LLRMLAGFESLTEGRILIDGEDMASMPPYRRPVNMMFQSYALFPHMTVENNVAFGLRQEG
CGKAEIRERVAAVLELVQMTRFAKRRPNQLSGGQQQRVALARSLVKRPKLLLLDEPMSAL
DKQIRQRTQVELVNILDQVDVTCIMVTHDQEEAMTMADRIGVMSDGLIVQTGSPLDVYEY
PSTRFAAEFIGSTNLFEGAVTESAADHVRIESAELMVPLYINHGIGSPSGAQVAVSIRPE
KVVLRRSRPDAAHNWAEGAVTHVVYMGSYSLYHVVIDSGKTIVANVSSLALADMGAPEVG
ERVAISWNSQSGVVLTQ
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