GapMind for catabolism of small carbon sources

 

Protein WP_048060749.1 in Methanothermobacter thermautotrophicus Delta H

Annotation: NCBI__GCF_000008645.1:WP_048060749.1

Length: 278 amino acids

Source: GCF_000008645.1 in NCBI

Candidate for 21 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) 40% 94% 193.4 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-tryptophan catabolism ecfA1 med Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 41% 93% 186.8 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
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% 91% 160.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
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% 91% 160.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 39% 88% 155.6 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 36% 69% 142.9 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 34% 87% 142.5 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 34% 87% 142.5 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 93% 141 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 33% 94% 140.6 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 33% 94% 140.6 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-asparagine catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 35% 100% 139.4 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-aspartate catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 35% 100% 139.4 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 35% 87% 138.7 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 83% 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% 235.0
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 83% 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% 235.0
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 35% 78% 130.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 35% 78% 130.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 34% 89% 128.6 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
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) 36% 82% 125.2 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 33% 88% 110.5 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 46% 235.0

Sequence Analysis Tools

View WP_048060749.1 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

MRIIEAVDIRYTYPDGTEALRGINFHAERGEVVALLGPNGAGKSTLFLHFNGILQPTSGK
IMIDGEELDYSKSGLIKARQKVGIVFQNPDDQLFAPRVDEDVAFGPLNMGLSEDEVEERV
RDALQKVGMLGYESKPPHHFSGGEKKRVAIAGIIAMKPDIMVLDEPTSGLDPRGASQILR
LLHNLNEEGMTIIISTHDVDLAPLYSDRIYIISDGEIISTGAPSEVFSDIDTIRGANLRL
PRIAHLVEILQKEDDLPFEEPYPLTIGEARRKLRNQLR

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