GapMind for catabolism of small carbon sources

 

Protein WP_011385763.1 in Magnetospirillum magneticum AMB-1

Annotation: NCBI__GCF_000009985.1:WP_011385763.1

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

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

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:

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