GapMind for catabolism of small carbon sources

 

Protein WP_091374146.1 in Mucilaginibacter mallensis MP1X4

Annotation: NCBI__GCF_900105165.1:WP_091374146.1

Length: 240 amino acids

Source: GCF_900105165.1 in NCBI

Candidate for 31 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 39% 91% 152.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 62% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 62% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 62% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 62% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 62% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 62% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 89% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 39% 89% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
L-arginine catabolism artP lo AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) 35% 96% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 56% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 34% 58% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 35% 54% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
trehalose catabolism thuK lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 35% 54% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 59% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 59% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 59% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 59% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 74% 128.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 34% 57% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 32% 58% 127.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 33% 60% 124.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 80% 104 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 87 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 87 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 87 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 87 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 87 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 83% 87 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 55% 247.3

Sequence Analysis Tools

View WP_091374146.1 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

MEPLITIKDIGRKYVIGTEIIHAIKSVSLTINKGEFVALMGPSGSGKSTLMNILGCLDTP
TKGDYILNGINVSQMTENQLAEVRNSEIGFVFQTFNLLPRNSALDNVALPLVYAGVSKEQ
RQERARQTLENVGLGHRVDHRPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTS
IEIMGLIEDIHDKGNTIILVTHEEDIAQHAHRIVRMRDGLVENDYVNPNIQRVDRTSVTL

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