GapMind for catabolism of small carbon sources

 

Protein AZOBR_RS30410 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS30410 ABC transporter ATP-binding protein

Length: 371 amino acids

Source: azobra in FitnessBrowser

Candidate for 42 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsD med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-glucose catabolism gtsD med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
lactose catabolism gtsD med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism gtsD med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism thuK med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-mannose catabolism TT_C0211 med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 48% 89% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
sucrose catabolism gtsD med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
sucrose catabolism thuK med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
trehalose catabolism gtsD med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
trehalose catabolism thuK med 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) 47% 96% 281.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 45% 96% 277.3 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 52% 71% 274.2 BitD, component of The iron transporter, BitABCDEF 43% 287.3
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 44% 99% 270 BitD, component of The iron transporter, BitABCDEF 43% 287.3
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 43% 94% 264.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 47% 80% 263.8 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism malK1 med 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) 44% 90% 262.3 BitD, component of The iron transporter, BitABCDEF 43% 287.3
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 93% 256.9 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 93% 256.9 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 49% 79% 256.9 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 75% 256.1 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 77% 255.8 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 52% 70% 255.4 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 42% 96% 251.9 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 48% 80% 250.4 BitD, component of The iron transporter, BitABCDEF 43% 287.3
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 48% 80% 250.4 BitD, component of The iron transporter, BitABCDEF 43% 287.3
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 48% 80% 250.4 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 44% 90% 249.6 BitD, component of The iron transporter, BitABCDEF 43% 287.3
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 44% 89% 246.5 BitD, component of The iron transporter, BitABCDEF 43% 287.3
trehalose catabolism malK med 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) 42% 91% 243.8 BitD, component of The iron transporter, BitABCDEF 43% 287.3
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 47% 77% 240.7 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism malK_Sm med MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 44% 79% 238.4 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 78% 236.1 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 78% 236.1 BitD, component of The iron transporter, BitABCDEF 43% 287.3
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 78% 236.1 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 78% 236.1 BitD, component of The iron transporter, BitABCDEF 43% 287.3
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 78% 236.1 BitD, component of The iron transporter, BitABCDEF 43% 287.3
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 45% 78% 236.1 BitD, component of The iron transporter, BitABCDEF 43% 287.3
L-proline catabolism opuBA med 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) 40% 75% 189.5 BitD, component of The iron transporter, BitABCDEF 43% 287.3
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) 52% 66% 260 BitD, component of The iron transporter, BitABCDEF 43% 287.3
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 49% 67% 258.5 BitD, component of The iron transporter, BitABCDEF 43% 287.3
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 33% 94% 129.4 BitD, component of The iron transporter, BitABCDEF 43% 287.3

Sequence Analysis Tools

View AZOBR_RS30410 at FitnessBrowser

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

MNHQFSPTSLAAGMESVGVRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTL
LRLIAGFNTAQRGAVTIGGRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRV
PRAEIERRVDAALDLVGLKHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLD
AKLRVQMRQELLSLQRKLGLTTIFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHP
ANLFVAGFLGTANVLEGQVRAVDGGTAFVMGGGVPIPLPHGVEPGAAGKLMFRPQNLFIR
QDGGPPRAGHVRLMGVVRHREFLGASIRYAVDIGGQQVQVDAPHQAGDALLPTDTPITLD
LAADKARFLRR

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