GapMind for catabolism of small carbon sources

 

Protein WP_075618489.1 in Paenisporosarcina indica PN2

Annotation: NCBI__GCF_001939075.1:WP_075618489.1

Length: 491 amino acids

Source: GCF_001939075.1 in NCBI

Candidate for 39 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism xacF hi Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 44% 97% 413.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 39% 349.0
D-galacturonate catabolism dopDH hi Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 44% 97% 413.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 39% 349.0
D-glucuronate catabolism dopDH hi Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 44% 97% 413.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 39% 349.0
D-xylose catabolism dopDH hi Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 44% 97% 413.7 betaine-aldehyde dehydrogenase (EC 1.2.1.8) 39% 349.0
L-valine catabolism mmsA med Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 40% 98% 338.6 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
4-hydroxybenzoate catabolism adh lo Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized) 40% 93% 347.8 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
2'-deoxyinosine catabolism adh lo Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized) 40% 93% 347.8 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
2-deoxy-D-ribose catabolism adh lo Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized) 40% 93% 347.8 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
ethanol catabolism adh lo Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized) 40% 93% 347.8 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-threonine catabolism adh lo Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized) 40% 93% 347.8 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
thymidine catabolism adh lo Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized) 40% 93% 347.8 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-tryptophan catabolism adh lo Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Brassica turgor-responsive/drought-induced gene 26 protein; Btg-26; EC 1.2.1.3 (characterized) 40% 93% 347.8 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 38% 97% 339.7 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 38% 97% 339.7 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 38% 97% 339.7 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 39% 97% 335.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 39% 97% 335.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 39% 97% 335.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 39% 97% 335.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 39% 97% 335.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-lysine catabolism amaB lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 39% 89% 335.1 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 97% 326.6 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 97% 326.6 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 97% 326.6 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 97% 326.6 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 38% 90% 308.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 38% 90% 308.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 38% 90% 308.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 38% 90% 308.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 38% 90% 308.9 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 95% 301.6 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 95% 301.6 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 95% 301.6 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 35% 97% 298.5 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 35% 97% 298.5 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 94% 275.4 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 35% 94% 275.4 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 32% 94% 211.1 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 32% 94% 211.1 Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 44% 413.7

Sequence Analysis Tools

View WP_075618489.1 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

Fitness BLAST: loading...

Sequence

MQLNNYIGGKWQEAGDAKYVSVTNPANGEELAQVRLSTQEDVNLAVAAAKEAQKKWALVP
APKRADYLYEVGRIMKEKKEHLAQVLTKEMGKVIEEGRGEVQEGIDMAFYMAGEGRRLFG
ETTPSELADKFAMSVRAPIGVVGLITPWNFPVAIATWKSFPAMVAGNTFLWKPATETPMM
AYEMAKVFEEAGIPDGVANIVFGSGADVGTAMIDHPDVKVISFTGSTETGRSVAERGGRN
LKKVSLEMGGKNAVIVMDDADLGLAVEGILWSAFGTAGQRCTACSRVIVHKDVKEELESR
LLTSMEQLTIGDGMDETVKIGPVINKKALEKIHSYVEIGKNEGATLLVGGEILSDGELAK
GNYYAPTLFTNVDRDSRIAQEEIFGPVVSLIEVSSLDEAIEVNNSVTFGLSSSIFSRDVN
TVFKAQRDLDTGIVYVNAGTTGAEIHLPFGGTKGTGNGHRDSGVAALDVYTEWKSIYVDF
SGKLQRAQIDN

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