GapMind for catabolism of small carbon sources

 

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:

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:

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:

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