GapMind for catabolism of small carbon sources

 

Protein WP_010182385.1 in Aquimarina agarilytica ZC1

Annotation: NCBI__GCF_000255455.1:WP_010182385.1

Length: 295 amino acids

Source: GCF_000255455.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 40% 89% 178.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 34% 73% 160.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 35% 69% 149.1 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 86% 147.9 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 34% 61% 146.4 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 37% 57% 145.2 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 34% 64% 144.8 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 34% 62% 135.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 34% 62% 135.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 34% 73% 118.6 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 61% 116.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4
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) 31% 98% 112.5 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 45% 255.4

Sequence Analysis Tools

View WP_010182385.1 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

MKKFLEVNQLAKKYPIKGEKNTFLSVFENINFSMQKGEFVCIVGHSGCGKSTILNNLAGL
DSPSSGNIIMDNKNVKKPSLERGVIFQNHSLLPWLSVLKNIKMAIACKFKELSTKEIEKR
ALHFLEMVELQDAVKKLPHELSGGMKQRVGIARAFALAPELLLMDEPFGALDALTRGKIQ
DKLLEICEKTNQTIFMITHDIDEAILLSDRILLMSNGPQARIAESVHVNIPKPRNRAEIV
NHPNYYLIRNHLVDFLINKSSEIAKGIQNNTIDDSEMPKNVSFTNTADLENRKAM

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