GapMind for catabolism of small carbon sources

 

Protein WP_011385763.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS17210 molybdenum import ATP-binding protein ModC

Length: 363 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 80% 155.6 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 80% 155.6 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 32% 83% 153.7 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 78% 152.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 78% 152.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 78% 152.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 78% 152.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 78% 152.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 33% 78% 152.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 34% 76% 148.3 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 32% 74% 147.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 33% 73% 147.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 88% 146.7 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 58% 144.4 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 34% 70% 144.1 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 31% 80% 144.1 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 32% 75% 142.9 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 30% 91% 142.5 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-mannose catabolism TT_C0211 lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 36% 56% 141.4 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 71% 141 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 31% 91% 140.2 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 64% 138.7 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 64% 138.7 ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins 45% 296.6

Sequence Analysis Tools

View WP_011385763.1 at NCBI

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MLDLDLRRRQGEFRLDVRLSAGPGVTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRV
LFDSRSGIDLPPEARRLGYVFQEHRLFPHLSVRGNLEFGQKLLPSAERTQSLDKVVELLG
IESLLDRRPAKLSGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARR
FSVPILYVSHSMDEVLRLADTLALMDGGKVAASGPLESLMGDPGLRPLTGRYEAGAVIGA
VVSSHDSGFGISRLAFDGGTLIVGRSELPVGAKVRLRIHARDVAIAIEPPDRVSIRNVLP
AIVVSVAPADSFLVDVILACGPTRFWVQITTLAQAQLNLVPGMRVHALIKALTIARGDVA
SVD

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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