GapMind for catabolism of small carbon sources

 

Protein YP_425390.1 in Rhodospirillum rubrum ATCC 11170

Annotation: NCBI__GCF_000013085.1:YP_425390.1

Length: 499 amino acids

Source: GCF_000013085.1 in NCBI

Candidate for 45 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism kauB med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 59% 99% 591.7 aldehyde dehydrogenase 63% 610.1
L-arginine catabolism puuC med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 59% 99% 591.7 aldehyde dehydrogenase 63% 610.1
L-citrulline catabolism puuC med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 59% 99% 591.7 aldehyde dehydrogenase 63% 610.1
putrescine catabolism puuC med gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 59% 99% 591.7 aldehyde dehydrogenase 63% 610.1
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 52% 98% 507.3 aldehyde dehydrogenase 63% 610.1
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 52% 98% 507.3 aldehyde dehydrogenase 63% 610.1
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 52% 98% 507.3 aldehyde dehydrogenase 63% 610.1
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 52% 98% 507.3 aldehyde dehydrogenase 63% 610.1
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 52% 98% 507.3 aldehyde dehydrogenase 63% 610.1
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 52% 98% 507.3 aldehyde dehydrogenase 63% 610.1
4-hydroxybenzoate catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 421 aldehyde dehydrogenase 63% 610.1
2'-deoxyinosine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 421 aldehyde dehydrogenase 63% 610.1
2-deoxy-D-ribose catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 421 aldehyde dehydrogenase 63% 610.1
ethanol catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 421 aldehyde dehydrogenase 63% 610.1
L-threonine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 421 aldehyde dehydrogenase 63% 610.1
thymidine catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 421 aldehyde dehydrogenase 63% 610.1
L-tryptophan catabolism adh med Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 45% 95% 421 aldehyde dehydrogenase 63% 610.1
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 92% 390.6 aldehyde dehydrogenase 63% 610.1
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 365.9 aldehyde dehydrogenase 63% 610.1
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 365.9 aldehyde dehydrogenase 63% 610.1
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 346.3 aldehyde dehydrogenase 63% 610.1
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 346.3 aldehyde dehydrogenase 63% 610.1
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 40% 96% 346.3 aldehyde dehydrogenase 63% 610.1
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 40% 95% 331.6 aldehyde dehydrogenase 63% 610.1
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 290.8 aldehyde dehydrogenase 63% 610.1
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 290.8 aldehyde dehydrogenase 63% 610.1
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 290.8 aldehyde dehydrogenase 63% 610.1
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 38% 97% 290.8 aldehyde dehydrogenase 63% 610.1
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 34% 98% 273.9 aldehyde dehydrogenase 63% 610.1
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 34% 98% 273.9 aldehyde dehydrogenase 63% 610.1
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 34% 98% 273.9 aldehyde dehydrogenase 63% 610.1
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 34% 98% 273.9 aldehyde dehydrogenase 63% 610.1
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 34% 94% 236.5 aldehyde dehydrogenase 63% 610.1
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 233.4 aldehyde dehydrogenase 63% 610.1
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 233.4 aldehyde dehydrogenase 63% 610.1
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 233.4 aldehyde dehydrogenase 63% 610.1
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 233.4 aldehyde dehydrogenase 63% 610.1
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 98% 233.4 aldehyde dehydrogenase 63% 610.1
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 33% 85% 225.3 aldehyde dehydrogenase 63% 610.1
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 33% 85% 225.3 aldehyde dehydrogenase 63% 610.1
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 33% 85% 225.3 aldehyde dehydrogenase 63% 610.1
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 33% 85% 225.3 aldehyde dehydrogenase 63% 610.1
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 33% 85% 225.3 aldehyde dehydrogenase 63% 610.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 95% 214.5 aldehyde dehydrogenase 63% 610.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 95% 214.5 aldehyde dehydrogenase 63% 610.1

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Sequence

MTQAAPPIDWTARARALRLPNHALIDGAPASAGDGATFDCVSPIDGRVLTRVAACGAADV
DRAVAAGRAAFEDRRWCGLSPAARKKILLAFAERIEAHRDELALLETLDMGKPIADSLAV
DVPATARCLRWYAEALDKVYGEVAPTGDDVLATITREPLGVVGVVVPWNFPMIMAAWKIA
PALAAGNSVVLKPAEQSPLTAIRLGELALEAGLPAGVLNVVPGLGPVTGRAIGLHPDIDG
AFFTGSTAVGKLFLSYSSQSNMKRLGLECGGKSAHIVLASCKNTTAAAQAAASAIFFNQG
EMCTAGSRLIVERAIADEVIEKVVAEAAFWRPGPPLDPATRMGALVDAEQTERVLGYIAL
GQDEGARLATGGSRAMAESGGCYVEPTIFTGVAPTMRIAREEIFGPVLSVITVESADEAV
RVANDSDYGLAAAVWSDDVTTLHRVAKRLRAGMVYANCYDADDITVPFGGFKQSGIGRDK
SLHAIDKYTELKTTWLRLG

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