GapMind for catabolism of small carbon sources

 

Protein WP_009488057.1 in Catellicoccus marimammalium M35/04/3

Annotation: NCBI__GCF_000313915.1:WP_009488057.1

Length: 255 amino acids

Source: GCF_000313915.1 in NCBI

Candidate for 42 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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% 150.2 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 89% 149.4 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 89% 149.4 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 89% 149.4 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 66% 149.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 66% 149.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 66% 149.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 66% 149.1 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 148.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 148.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 148.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 148.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 148.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 148.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 147.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 35% 94% 147.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 91% 143.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 91% 143.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
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) 36% 85% 142.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
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) 36% 85% 142.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 55% 142.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
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) 36% 85% 142.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
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) 36% 85% 142.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
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) 36% 85% 142.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
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) 36% 85% 142.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 36% 88% 140.6 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 36% 88% 140.6 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 91% 137.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 60% 136.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 34% 85% 132.5 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 54% 131.7 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 58% 127.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 58% 127.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 58% 127.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 58% 127.9 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 33% 58% 126.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 54% 126.3 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
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) 35% 89% 124.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 36% 65% 119.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 73% 112.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 53% 104.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 33% 73% 99.8 Lmo2114 protein, component of ABC multidrug resistance efflux pump, AnrAB 52% 281.6

Sequence Analysis Tools

View WP_009488057.1 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

MVLECLRVQNLEKYYGNKSQMTKALENIEFSVEEGEFVGIMGPSGSGKSTLLNCIATLER
PTSGTVCLNGEAIDYRKERKLEKIRKEHLGFIFQEYNLLSTLTAYENIALSLTIQNQSPS
TIQKRISLLAQQLGIQEILGKYPAELSGGQQQRVAAARALVKNPDLILADEPTGALDSKS
AYQLLEQLEVLQQENQATILMVTHDAFTASFAQRILFIKDGKIFSEIEKGNDTREQFFQR
ILEVIAVIGGGEDVF

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