Protein WP_013840601.1 in Desulfotomaculum ruminis DSM 2154
Annotation: NCBI__GCF_000215085.1:WP_013840601.1
Length: 515 amino acids
Source: GCF_000215085.1 in NCBI
Candidate for 34 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-arginine catabolism | putA | hi | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 60% | 100% | 613.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-arginine catabolism | putA | hi | pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) | | 100% | 764.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-arginine catabolism | rocA | hi | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 60% | 100% | 613.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-arginine catabolism | rocA | hi | pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) | | 100% | 764.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-citrulline catabolism | putA | hi | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 60% | 100% | 613.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-citrulline catabolism | putA | hi | pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) | | 100% | 764.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-citrulline catabolism | rocA | hi | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 60% | 100% | 613.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-citrulline catabolism | rocA | hi | pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) | | 100% | 764.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-proline catabolism | putA | hi | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) | 60% | 100% | 613.2 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-proline catabolism | putA | hi | pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01237) | | 100% | 764.4 | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 | 38% | 312.0 |
L-arabinose catabolism | xacF | lo | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 38% | 98% | 312 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
D-galacturonate catabolism | dopDH | lo | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 38% | 98% | 312 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
D-glucuronate catabolism | dopDH | lo | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 38% | 98% | 312 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
D-xylose catabolism | dopDH | lo | Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) | 38% | 98% | 312 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-fucose catabolism | aldA | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 36% | 97% | 298.5 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-rhamnose catabolism | aldA | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 36% | 97% | 298.5 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-threonine catabolism | aldA | lo | lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) | 36% | 97% | 298.5 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-arginine catabolism | gabD | lo | Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) | 33% | 90% | 242.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-citrulline catabolism | gabD | lo | Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) | 33% | 90% | 242.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
putrescine catabolism | gabD | lo | Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized) | 33% | 90% | 242.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-valine catabolism | mmsA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 33% | 100% | 241.5 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-phenylalanine catabolism | pad-dh | lo | aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) | 33% | 88% | 237.7 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-isoleucine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 34% | 97% | 236.9 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
myo-inositol catabolism | mmsA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 34% | 97% | 236.9 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
propionate catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 34% | 97% | 236.9 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-threonine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 34% | 97% | 236.9 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-valine catabolism | iolA | lo | methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) | 34% | 97% | 236.9 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-arginine catabolism | patD | lo | aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) | 33% | 88% | 235.7 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-citrulline catabolism | patD | lo | aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) | 33% | 88% | 235.7 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
putrescine catabolism | patD | lo | aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) | 33% | 88% | 235.7 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-arginine catabolism | kauB | lo | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 34% | 92% | 229.6 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-arginine catabolism | puuC | lo | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 34% | 92% | 229.6 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-citrulline catabolism | puuC | lo | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 34% | 92% | 229.6 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
putrescine catabolism | puuC | lo | 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) | 34% | 92% | 229.6 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
4-hydroxybenzoate catabolism | praB | lo | 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) | 32% | 100% | 228.4 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-tryptophan catabolism | praB | lo | 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) | 32% | 100% | 228.4 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-lysine catabolism | amaB | lo | L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) | 31% | 85% | 180.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-arginine catabolism | astD | lo | Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) | 32% | 92% | 175.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
L-citrulline catabolism | astD | lo | Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) | 32% | 92% | 175.3 | L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) | 60% | 613.2 |
Sequence Analysis Tools
View WP_013840601.1 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
MLTDYKNEPFLDFSNEKVADSFKKALQEVKAKLGSRYPLIINGKAVETGEEVISLNPSAS
DQVVGYVAKASLQEAKLALESAQEAFARWSRVKPEERARYLFKAAAIMRRRKMELSAWMV
FEAGKNWAEADGDTAEAIDFLEFYGREMCRLAEPQPLVRIFGEDNRLKYIPLGVGLVIPP
WNFPLAIMAGMTAAAIVTGNTVVLKPASNTPVIAAKFIEILQEAGLPDGVVNYLPGSGGA
IGDYLVSSPQIRFINFTGSKEVGLRISELAAKMVPGQKAIKRVVAEMGGKDAIIVDSSSD
LEEAAAAIVASAFGFQGQKCSACSRAIILDDVYDRIVELVIDKTKKLTVGPAVDNYPVGP
VTDSNSLKRIKSYIEIGKKEGTLQVGGETLEHMGGYFVQPTVITDVPPNATIAQEEIFGP
VLAVIRAKDFSHALDIANGTEYGLTGSVFSRNRANLERAAREFHVGNLYFNRKCTGALVG
VHPFGGFNMSGTDSKAGGRDYLLLFSQAKAISEKY
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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