GapMind for catabolism of small carbon sources

 

Protein WP_027699581.1 in Weissella oryzae SG25

Annotation: NCBI__GCF_000691805.2:WP_027699581.1

Length: 651 amino acids

Source: GCF_000691805.2 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-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 42% 90% 157.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-arginine catabolism artP lo histidine transport ATP-binding protein hisP (characterized) 38% 89% 159.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 38% 89% 159.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-lysine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 38% 89% 159.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 86% 158.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 74% 157.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 38% 89% 151.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 38% 89% 151.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 36% 84% 143.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 88% 136.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 78% 119.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 79% 90.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 31% 291.6

Sequence Analysis Tools

View WP_027699581.1 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

MAFLTLRDIQKSYFLGKEEFPVLKGINLEFELGEFVSILGESGGGKSTLMNIIGGLDREF
DGEVTFEGTLLDHKKEKQLDEYRRGTIGYIYQAYNLISHLTVLDNVLVSLEMTNLSQKER
INRATELLERVGLGDQMKKHPNQLSGGQKQRVAIARALAADPKIIIADEPTGALDSQNTA
EVLTLLEEIAKEGKLVIAVTHSQEVANHGTRIVHLADGKIDGDQRLKPAYPVPTDNVQIA
DRPLKASASYSNAFKHLRYTFWRNSLIMLGTAIGLFAVMLFSGLGNGIKAYIADQVNSLA
NPTAVTVQRYSKNANSQRPGQGEGSLTISNSQVKQLADLTHVKQAEPGYVLANGQFRLGT
TTYALNNMSTWSASYQTKIIKAGTKPGKDEMVVDKNTVAKQYSSKDWKSIVGKKVTVTWV
AAKADGTPVPVSRELTISGVADFGHNQVTNLTTYQTVQAANKSVGASTDAAMVTVKVNDA
KNVDSVAKKINAIKQDGKRQFNAITIGDILGTINTIVTLATTVLAAIAGISLVVSALMII
VTMFMSVSERTKEIGILRALGESKKDVRRLFTAESLLIGFFSYILALILAFGLGAILNNV
LYKIAKFDMIQLSLTNIITTLILAIVIAYVAALLPARRAAKLNPIDALSAD

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