GapMind for catabolism of small carbon sources

 

Protein WP_156477079.1 in Collimonas arenae Ter10

Annotation: NCBI__GCF_001584165.1:WP_156477079.1

Length: 255 amino acids

Source: GCF_001584165.1 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 53% 95% 258.1 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-arginine catabolism artP med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 52% 97% 250.8 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 52% 97% 250.8 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 51% 99% 246.5 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 53% 98% 241.5 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-lysine catabolism hisP med ABC transporter for L-Lysine, ATPase component (characterized) 52% 97% 240 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 50% 97% 237.7 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 50% 97% 237.7 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-asparagine catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 53% 99% 234.2 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-aspartate catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 53% 99% 234.2 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 50% 97% 233.8 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-citrulline catabolism PS417_17605 med 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) 50% 91% 232.6 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-asparagine catabolism aapP med 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) 48% 93% 232.3 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-aspartate catabolism aapP med 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) 48% 93% 232.3 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-glutamate catabolism aapP med 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) 48% 93% 232.3 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-histidine catabolism aapP med 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) 48% 93% 232.3 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-leucine catabolism aapP med 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) 48% 93% 232.3 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-proline catabolism aapP med 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) 48% 93% 232.3 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 48% 90% 231.5 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 48% 90% 231.5 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 49% 94% 228 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-histidine catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 42% 83% 159.8 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 42% 83% 159.8 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-tryptophan catabolism ecfA2 med Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 41% 77% 133.3 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 38% 77% 133.3 TcyC (YckI), component of Uptake system for L-cystine 55% 265.0

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Sequence

MISIRNLKKCFGDNVVLKDISLEISKGSVVAMIGPSGSGKSTLLRCINLLTIPDAGTVNV
GGQSIAFDGKHTKLPKAKDLAHFRSKTGMVFQHFNLFPHMTVRQNVMEGMVTVLKIPKQD
ARITADALLQRVGLSDRADAYPGMLSGGQKQRVAIARALAMKPDVMLFDEATSALDPELV
GEVLSVIRSLAADGMTMILVTHEIAFAREVADQVIFMRDGVVVECGPPSVVIDNPEKEAT
RSFLSRFKTANINAA

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