GapMind for catabolism of small carbon sources

 

Protein GFF5296 in Pseudomonas simiae WCS417

Annotation: PS417_27115 transporter

Length: 380 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 63% 96% 425.2 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 41% 257.3
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 92% 246.5 PotG aka B0855, component of Putrescine porter 63% 425.2
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 92% 246.5 PotG aka B0855, component of Putrescine porter 63% 425.2
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) 42% 89% 244.6 PotG aka B0855, component of Putrescine porter 63% 425.2
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 75% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 229.9 PotG aka B0855, component of Putrescine porter 63% 425.2
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) 38% 92% 221.9 PotG aka B0855, component of Putrescine porter 63% 425.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 207.2 PotG aka B0855, component of Putrescine porter 63% 425.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 207.2 PotG aka B0855, component of Putrescine porter 63% 425.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 207.2 PotG aka B0855, component of Putrescine porter 63% 425.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 207.2 PotG aka B0855, component of Putrescine porter 63% 425.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 207.2 PotG aka B0855, component of Putrescine porter 63% 425.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 207.2 PotG aka B0855, component of Putrescine porter 63% 425.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 207.2 PotG aka B0855, component of Putrescine porter 63% 425.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 87% 207.2 PotG aka B0855, component of Putrescine porter 63% 425.2
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 35% 85% 183 PotG aka B0855, component of Putrescine porter 63% 425.2
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 39% 90% 170.2 PotG aka B0855, component of Putrescine porter 63% 425.2
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 39% 90% 170.2 PotG aka B0855, component of Putrescine porter 63% 425.2
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% 78% 138.7 PotG aka B0855, component of Putrescine porter 63% 425.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 80% 133.7 PotG aka B0855, component of Putrescine porter 63% 425.2

Sequence Analysis Tools

View GFF5296 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

MAVASGAYKKALEGDQTPKKVLVKIDRVTKKFDETIAVDDVSLEIKKGEIFALLGGSGSG
KSTLLRMLAGFERPTEGRIYLDGEDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLQ
QDKIPKAEIDARVAEMLKLVQMSQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPM
GALDKKLRSQMQLELVEIIERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQIGSPIDI
YETPTSRLVCEFIGNVNIFDTQVVDDAEGHAVLKCPDLDRDIYVGYGIATSVEDKSVTYA
IRPEKLLVTTEMPTCEHNWSSGKVHDIAYLGGHSVFYVELPSGKLVQSFVANAERRGQRP
TWGDQVYVWWEDDSGVVLRS

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