GapMind for catabolism of small carbon sources

 

Protein WP_011383734.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS06730 nitrate ABC transporter ATP-binding protein

Length: 452 amino acids

Source: GCF_000009985.1 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-histidine catabolism Ac3H11_2560 hi ABC transporter for L-Histidine, ATPase component (characterized) 42% 98% 208 ABC transporter for nitrate, ATPase component 40% 193.7
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) 40% 75% 142.9 ABC transporter for L-Histidine, ATPase component 42% 208.0
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) 40% 75% 142.9 ABC transporter for L-Histidine, ATPase component 42% 208.0
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 43% 54% 161.8 ABC transporter for L-Histidine, ATPase component 42% 208.0
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) 40% 57% 159.5 ABC transporter for L-Histidine, ATPase component 42% 208.0
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 72% 155.2 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 72% 155.2 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 83% 150.6 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 83% 150.6 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 39% 58% 150.6 ABC transporter for L-Histidine, ATPase component 42% 208.0
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 83% 150.6 ABC transporter for L-Histidine, ATPase component 42% 208.0
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 83% 150.6 ABC transporter for L-Histidine, ATPase component 42% 208.0
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 75% 147.9 ABC transporter for L-Histidine, ATPase component 42% 208.0
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 39% 61% 146.4 ABC transporter for L-Histidine, ATPase component 42% 208.0
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 39% 61% 146.4 ABC transporter for L-Histidine, ATPase component 42% 208.0
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 40% 54% 145.2 ABC transporter for L-Histidine, ATPase component 42% 208.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 34% 76% 144.4 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 59% 142.5 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 53% 138.7 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 37% 63% 138.3 ABC transporter for L-Histidine, ATPase component 42% 208.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 54% 132.5 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 54% 132.5 ABC transporter for L-Histidine, ATPase component 42% 208.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 54% 132.5 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 54% 132.5 ABC transporter for L-Histidine, ATPase component 42% 208.0
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 40% 58% 132.1 ABC transporter for L-Histidine, ATPase component 42% 208.0
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 30% 69% 94.4 ABC transporter for L-Histidine, ATPase component 42% 208.0

Sequence Analysis Tools

View WP_011383734.1 at NCBI

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MADITTSTALLDLRGVRKTFLTPDRRERTVLEGVDFKLEEGEIVALLGKSGSGKSTLLRI
MAGLIKANGGEVKYRGHLMTGPAKGISMVFQSFALFPWLTVEENVELGLEAAGVAKAERE
ERANEAIDLIGLGGYESAYPKELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSET
LREDLLELWDERKIPTKGILLVSHNIEEAVSMADRVLVFSSDPGRVRAEIRVNLPRPRDT
ESAAFRQIVDEVYTLMTANVRGGGLGAAEQLTLGYRLPDTTPGKMAGLLETVAEAPFNGR
ADLPQLAEETELEDDQLFHLFEGLRVLGLARIAAGDIFVTPAGQAFVEADDAVRKDLFAE
ALVKHIPLAAHIRRVLDERKDHRAPEDRFLQELQDYLTDDEAERVLETTITWGRYAEIFD
YDYNAGVLMLPEEVVEEMEAEEEARDESGLRE

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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