GapMind for catabolism of small carbon sources

 

Protein WP_011022097.1 in Methanosarcina acetivorans C2A

Annotation: NCBI__GCF_000007345.1:WP_011022097.1

Length: 267 amino acids

Source: GCF_000007345.1 in NCBI

Candidate for 26 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 96% 141.4 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 96% 141.4 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 35% 96% 141.4 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
2'-deoxyinosine catabolism nupA lo RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) 35% 53% 129.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 33% 96% 124.4 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 122.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 122.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 122.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
D-cellobiose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 32% 50% 115.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
D-glucose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 32% 50% 115.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
lactose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 32% 50% 115.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
D-maltose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 32% 50% 115.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
sucrose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 32% 50% 115.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
trehalose catabolism mglA lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 32% 50% 115.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
D-xylose catabolism xylG lo Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 32% 50% 115.9 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 90% 114.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 90% 114.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 90% 114.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-isoleucine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 113.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-valine catabolism natA lo NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 94% 113.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-arginine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 84% 110.5 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-glutamate catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 84% 110.5 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-histidine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 84% 110.5 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 92% 93.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 92% 93.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 92% 93.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 42% 192.2

Sequence Analysis Tools

View WP_011022097.1 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

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Sequence

MQNILSVKSLTKKFDDLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGE
ILINGYNALKEQDKARSSFGIVFQDYSLDSELTAYENMEYHSVIYKVPKAEREERIKTAL
EIVGLWNRRNDLVKKYSGGMKRRLEIARALVHYPKVLFLDEPTVGLDPQTRMSIWNHIKR
LNEERKMTIFLTTHYMDEAEAMADKIAIIDHGKIIESGTLAEIMERTETESLEESFLKLT
GRDIRDENGNGGDKMRFMRGIGRRHGH

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