GapMind for catabolism of small carbon sources

 

Protein WP_015819670.1 in Teredinibacter turnerae T7901

Annotation: NCBI__GCF_000023025.1:WP_015819670.1

Length: 535 amino acids

Source: GCF_000023025.1 in NCBI

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannose catabolism TM1749 med TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 52% 78% 260.8 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
D-mannose catabolism TM1750 med TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 40% 76% 195.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 38% 77% 190.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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) 40% 96% 183 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 35% 77% 158.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 38% 72% 156.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 38% 56% 144.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 96% 142.5 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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) 35% 98% 142.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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) 35% 98% 142.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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) 35% 98% 142.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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) 35% 98% 142.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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) 35% 98% 142.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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) 35% 98% 142.1 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 35% 96% 139.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 35% 96% 139.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 33% 98% 139 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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) 34% 78% 138.7 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
L-arginine catabolism artP lo Histidine transport ATP-binding protein HisP (characterized) 34% 98% 136.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 34% 98% 136.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 32% 61% 126.3 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
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% 123.6 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 34% 86% 114.4 Glutathione import ATP-binding protein GsiA; EC 7.4.2.10 47% 485.7

Sequence Analysis Tools

View WP_015819670.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Fitness BLAST: loading...

Sequence

MSLLSVSNLTTNFYTREGVTNAVKNVSFELEAGKILGIVGESGSGKSVSCYSILGLIPSP
PGKVESGTAVFEGKDLLKMSEKELREVRGRKISMIFQDPMTSLNPFMTIGKQLMEAYRLH
FKADKKTARQKALKALQEVGIVNAENRLDAYPHEFSGGMRQRVMIAMALITEPKLLVADE
PTTALDVTIQAQILELIKKLQASHNLGVIFITHDLAVISKLADDIMVMKSGEVVEKGTAQ
EVFTQQKHPYTQKLIAAVPDSAKPVPAQTVLNEKPLVRVESVNKTYVTHSGGMFSQKHES
FKAVDNISLEIKRGEILGLVGESGSGKSTLGRSIIRLIESESDGIFIGNQQVDRLSPRQL
RDARKNFQMIFQDPFASLNPRYTVYDTLAEPLLKHKIATPKNIVQKINELLDDVGLERKH
IRKYPHEFSGGQRQRIAIARALAPDPQFIVADEPVSALDVTIQAQILELILNLAEKRGLT
MLFISHDLAVVRYLCDRVIVMNRGKIVEQGETESLFNNPQQDYTRQLLAAIPQFA

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