GapMind for catabolism of small carbon sources

 

Protein WP_048079924.1 in Methanobacterium veterum MK4

Annotation: NCBI__GCF_000745485.1:WP_048079924.1

Length: 279 amino acids

Source: GCF_000745485.1 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-tryptophan catabolism ecfA2 med Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 42% 95% 205.7 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-tryptophan catabolism ecfA1 med Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 40% 93% 189.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 38% 90% 162.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-asparagine catabolism glnQ lo 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) 38% 93% 159.8 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-glutamate catabolism gltL lo 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) 38% 93% 159.8 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 100% 148.3 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 100% 148.3 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 96% 147.5 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 95% 147.1 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 95% 147.1 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 35% 92% 144.4 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 86% 138.3 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 86% 138.3 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 34% 96% 137.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
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) 32% 77% 134.8 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
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) 34% 82% 124 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 77% 121.3 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 88% 117.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 88% 117.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 88% 117.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 88% 117.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 88% 117.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 88% 117.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 110.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 110.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 110.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 110.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 110.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 110.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2
2'-deoxyinosine catabolism nupA lo Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) 33% 53% 107.8 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 234.2

Sequence Analysis Tools

View WP_048079924.1 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

Fitness BLAST: loading...

Sequence

MNIIETKDIAYSYPDGTKALDKVNFKAEEGKIIALLGPNGAGKSTLFLHFNGILRPTSGK
VLLNGDEIKYDKKALMHVRQNVGIVFQNPDDQLFAPTVVEDVAFGPMNLGLSKEEVEKRV
DESLKRVGMEEFKKKAPHHLSGGQKKRVAIAGILAMNPRIMVLDEPTSGLDPKGASQILK
ILYELNKEGMTIIISTHDVDLVPLYAYSVYIISKGKIIKEGNPQEVFGDVKTIREANLRL
PRIAHLMEILEKEDKLPFDKPYPLTIGEARKKLRDHFDD

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