GapMind for catabolism of small carbon sources

 

Protein WP_074201578.1 in Sulfurivirga caldicuralii DSM 17737

Annotation: NCBI__GCF_900141795.1:WP_074201578.1

Length: 262 amino acids

Source: GCF_900141795.1 in NCBI

Candidate for 30 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 lo GluA aka CGL1950, component of Glutamate porter (characterized) 37% 91% 131.3 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 33% 98% 131 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 59% 124 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 33% 98% 120.2 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 33% 98% 120.2 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 86% 119.4 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 86% 119.4 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 86% 119.4 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 86% 119.4 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 86% 119.4 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 34% 86% 119.4 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 33% 82% 119 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 53% 114.4 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 31% 59% 113.6 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 34% 87% 113.2 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 32% 98% 113.2 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 32% 98% 113.2 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 60% 112.5 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 60% 112.5 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 60% 112.5 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 60% 112.5 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 60% 112.5 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 60% 112.5 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 60% 112.5 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 31% 98% 110.9 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 32% 58% 108.2 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 30% 62% 106.7 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 30% 62% 106.7 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 31% 74% 105.9 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 32% 85% 94.4 phosphate import ATP-binding protein pstB; EC 3.6.3.27 61% 305.1

Sequence Analysis Tools

View WP_074201578.1 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

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Sequence

MDANLMMEVKDFSFTYPNAPKPSLKHINLRVVKNRITALIGPSGCGKSTLLRAMNRIHDL
YPGCKYEGAINLQCVDGSVKNILEWTKENDLIRLRQKVGMIFQKPTPFPMSIYDNIAYGL
KLQGIRSKSELDDRVEEALRDGALWNEVKDRLKDDARGLSGGQQQRLCIARSVALRPDVI
LFDEPTSALDPISTVAIEEMIMELREQYTICIVTHNMQQAARISDYTAFMYLGELIEYDE
TDTIFTNPSQKQTEDYITGRFG

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:

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