GapMind for catabolism of small carbon sources

 

Protein GFF1380 in Marinobacter adhaerens HP15

Annotation: HP15_1347 sulfate/thiosulfate transporter subunit

Length: 362 amino acids

Source: Marino in FitnessBrowser

Candidate for 31 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 45% 79% 245 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 42% 88% 238.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 81% 228.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 81% 228.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 81% 228.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 81% 228.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 81% 228.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 81% 228.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 41% 75% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 40% 77% 213.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 72% 202.2 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 72% 202.2 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 72% 202.2 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
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) 39% 86% 222.2 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 39% 85% 216.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 44% 68% 216.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 88% 215.7 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 86% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 79% 207.6 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 92% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 92% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 92% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 92% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 92% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 92% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 92% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 92% 204.9 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 38% 83% 191.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 36% 93% 175.6 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 34% 90% 164.5 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 79% 144.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0

Sequence Analysis Tools

View GFF1380 at FitnessBrowser

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

MSIEIQGINKFFDKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIR
FSGKDVTDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDL
LEMVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLR
SLHDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQV
NVLSGKIRDGVMRQGDAWIRLPEGCENDDAQLYLRPHEVRLTQSASDDAHLPFRIEAINL
IGAEVRIELKPDGWECEELWEVGISHTEFNARQPQRGDRCFAVPDVGHLFCEHSQEPKTL
VW

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