GapMind for catabolism of small carbon sources

 

Protein WP_019614605.1 in Psychromonas ossibalaenae JAMM 0738

Annotation: NCBI__GCF_000381745.1:WP_019614605.1

Length: 466 amino acids

Source: GCF_000381745.1 in NCBI

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-xylose catabolism xylT hi D-xylose-proton symporter (characterized) 55% 97% 498 Major myo-inositol transporter, IolT1, of 456 aas 44% 392.9
myo-inositol catabolism iolT med Major myo-inositol transporter, IolT1, of 456 aas (characterized) 44% 97% 392.9 D-xylose-proton symporter 55% 498.0
L-arabinose catabolism araE med Arabinose-proton symporter; Arabinose transporter (characterized) 40% 95% 347.1 D-xylose-proton symporter 55% 498.0
D-galactose catabolism galP med Arabinose-proton symporter; Arabinose transporter (characterized) 40% 95% 347.1 D-xylose-proton symporter 55% 498.0
D-cellobiose catabolism MFS-glucose med Glucose facilitated diffusion protein (characterized) 42% 98% 339.3 D-xylose-proton symporter 55% 498.0
D-glucose catabolism MFS-glucose med Glucose facilitated diffusion protein (characterized) 42% 98% 339.3 D-xylose-proton symporter 55% 498.0
lactose catabolism MFS-glucose med Glucose facilitated diffusion protein (characterized) 42% 98% 339.3 D-xylose-proton symporter 55% 498.0
D-maltose catabolism MFS-glucose med Glucose facilitated diffusion protein (characterized) 42% 98% 339.3 D-xylose-proton symporter 55% 498.0
sucrose catabolism MFS-glucose med Glucose facilitated diffusion protein (characterized) 42% 98% 339.3 D-xylose-proton symporter 55% 498.0
trehalose catabolism MFS-glucose med Glucose facilitated diffusion protein (characterized) 42% 98% 339.3 D-xylose-proton symporter 55% 498.0
D-fructose catabolism glcP lo Glucose/fructose:H+ symporter, GlcP (characterized) 40% 97% 317.4 D-xylose-proton symporter 55% 498.0
sucrose catabolism glcP lo Glucose/fructose:H+ symporter, GlcP (characterized) 40% 97% 317.4 D-xylose-proton symporter 55% 498.0
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 33% 91% 236.5 D-xylose-proton symporter 55% 498.0
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 87% 231.1 D-xylose-proton symporter 55% 498.0
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 87% 231.1 D-xylose-proton symporter 55% 498.0
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 31% 87% 231.1 D-xylose-proton symporter 55% 498.0
D-sorbitol (glucitol) catabolism SOT lo polyol transporter 5 (characterized) 31% 87% 231.1 D-xylose-proton symporter 55% 498.0
xylitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 87% 231.1 D-xylose-proton symporter 55% 498.0
D-mannose catabolism STP6 lo The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized) 31% 94% 227.3 D-xylose-proton symporter 55% 498.0
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 32% 86% 209.5 D-xylose-proton symporter 55% 498.0
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 37% 59% 208 D-xylose-proton symporter 55% 498.0
D-glucosamine (chitosamine) catabolism SLC2A2 lo Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized) 30% 77% 189.1 D-xylose-proton symporter 55% 498.0
D-fructose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 31% 77% 181.8 D-xylose-proton symporter 55% 498.0
sucrose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 31% 77% 181.8 D-xylose-proton symporter 55% 498.0

Sequence Analysis Tools

View WP_019614605.1 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

MKDNINVLHVTIVVALGGLLFGYDTAVISGATGSLTHFFGLSATELGFAASSALVGCFIG
ALVAGKISDSMGRRGALKIAATLFLISAIGTAVPDNYWVFVFFRIVGGIGVGIASMVSPM
YIAEVAPPNKRGALVSCNQFAIIFGMLVVYFVNYGIALAGTEVWLNTVGWRYMFASECIP
ALLFLVLLFTVPETPRWLALKGRNQEARNLLRALNKNEDIEEQWQGIQSSLGDTKGKVSI
AALGMMGVLVIGIMLSVLQQVTGINVFLYYAPEIFKSFSDSSTDTALLQTILIGAVNLTF
TAIAIFTVDKFGRRPLMIIGAGAMAVSMIAIGTAAYSNAIGGYLLFFVLLYIAAFALSLG
PVTWVLLSEIFPNSIRSKALSIAVFAQWFANFVVSQSFPMMNDSNGYLFQTYNGGFPFWL
YGFFGVFTVYFIWKFVPETKGKSLEDLEKIWVRKQEKTTVKEAQII

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