GapMind for catabolism of small carbon sources

 

Protein 6938573 in Shewanella amazonensis SB2B

Annotation: Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)

Length: 1058 amino acids

Source: SB2B in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 100% 100% 2068.1
L-arginine catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 100% 100% 2068.1
L-arginine catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710.6
L-arginine catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 100% 100% 2068.1
L-arginine catabolism rocA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710.6
L-citrulline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 100% 100% 2068.1
L-citrulline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 100% 100% 2068.1
L-citrulline catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710.6
L-citrulline catabolism rocA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 100% 100% 2068.1
L-citrulline catabolism rocA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710.6
L-proline catabolism put1 hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 100% 100% 2068.1
L-proline catabolism putA hi L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 100% 100% 2068.1
L-proline catabolism putA hi delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 710.6
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 92% 205.7 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 100% 2068.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 92% 205.7 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 100% 2068.1
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 32% 93% 184.9 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 100% 2068.1
L-lysine catabolism amaB lo Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) 30% 87% 169.9 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) 100% 2068.1

Sequence Analysis Tools

View 6938573 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

MFKASEVLAGRYDNANLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDL
VAKVRQYEKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGA
KWDEHMSKSDSVLVNASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYA
AMKIMGKQFVLGRTIEEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQA
LGTAKFDESEAPRPTISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQID
AEEVDRLELSLKLFKKLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPL
RLVKGAYWDSELKWAQQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHN
AQTVAAITAMVGDRKFEFQRLHGMGQELYDTVLAEAAVPTVRIYAPIGAHKDLLPYLVRR
LLENGANTSFVHKLVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGL
NMNIISESEPFFAALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEA
TIEQAIAGADKAFASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDE
VREAVDFCRYYAVQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQV
AAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIG
GVCFTGSTTTAKVINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTS
AGQRCSALRVLYLQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHI
DHIKQVGRLIHQLSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKV
IDDINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTG
PKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDAD

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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