GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS23420 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS23420 acetoacetyl-CoA synthase

Length: 1021 amino acids

Source: BFirm in FitnessBrowser

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2-deoxy-D-ribonate catabolism aacS med acetoacetate-CoA ligase (EC 6.2.1.16) (characterized) 40% 98% 423.7 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
2-deoxy-D-ribonate catabolism aacS hi acetoacetate-CoA ligase (EC 6.2.1.16) (TIGR01217) 97% 583.8 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
2-deoxy-D-ribose catabolism aacS med acetoacetate-CoA ligase (EC 6.2.1.16) (characterized) 40% 98% 423.7 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
2-deoxy-D-ribose catabolism aacS hi acetoacetate-CoA ligase (EC 6.2.1.16) (TIGR01217) 97% 583.8 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
L-leucine catabolism aacS med acetoacetate-CoA ligase (EC 6.2.1.16) (characterized) 40% 98% 423.7 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
L-leucine catabolism aacS hi acetoacetate-CoA ligase (EC 6.2.1.16) (TIGR01217) 97% 583.8 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
L-phenylalanine catabolism aacS med acetoacetate-CoA ligase (EC 6.2.1.16) (characterized) 40% 98% 423.7 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
L-phenylalanine catabolism aacS hi acetoacetate-CoA ligase (EC 6.2.1.16) (TIGR01217) 97% 583.8 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
L-tyrosine catabolism aacS med acetoacetate-CoA ligase (EC 6.2.1.16) (characterized) 40% 98% 423.7 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2
L-tyrosine catabolism aacS hi acetoacetate-CoA ligase (EC 6.2.1.16) (TIGR01217) 97% 583.8 4-hydroxybenzoyl-acetyl-CoA synthetase 35% 343.2

Sequence Analysis Tools

View BPHYT_RS23420 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

MNHENFVGASMRMYAREPVFQNLPERVAGSRMSRFTAALENFTGERFADYPELHAYSTRE
FRRFWQCFLQWTEGMEWGGKAEPACVGDECETASFFPNVELNYAQSVLGSKIAPDESPAL
TARYADGRRETMTRGELRERVARLACSLNELGLCPGDRAVAIMRNDAHAIIAALAVTALG
ATLSTAAPETGVQAILDRFEPLEPRILFAHTTQRSFDTAGSIASHVAAVAAALPTLTHVV
CLDETPLPSTVSQPQHSLRDLIVQGDAARFAWRRFPFNHPLFIMFSSGTTGKPKCIVHGA
GGTLLEHLKEHQLHSDLGPGDKLYFHTSCSWMMWNWQLSALASGVEIVTYDGPVSEVDTL
WRMVADERVTVFGTSPAYLKMCEDAGLKPGEQFGLHALRAMMSTGAVLYDSQFEWVRAYV
KPLQLQSISGGTDIIGCFVLGNPNLPVYAGEAQCRSLGLDVQAWNEGAPTSMTGELVCVN
PFPSRPLGFFGDADGSRFHAAYFKANPGVWTHGDIIEFSAQGSARLHGRSDGVLNVRGIN
VSPGEIYRIVSGIGEINQSMVVAQTTHDASGSGQRVVLLLVLRRGAKMSAALASRVRREL
MLQGSAALVPDVIAEVEALPVTHNGKASEAAARDAVNGLPVRNLSSLANPGCVEKISAHP
ALARTRRELPEPGDSAEQVEVYLCALWEQLFSFSPVSRDDNFFELGGHSLLAAQMLAEIR
LATGRTLPLATLIIAPTIARLATVITGERTQDAHPNVVPMRAGRGRPVFMLHSITGSVME
CLTLAGALASERPVYGLQARGLDGDEEPQRCVEEMARVYVRQMRAVQPRGPYALVGYSFG
GLVAFEMAQQLVAAGEKIELLCLLDTYVDERYLPLHEWLSFQYEVMAERVRAFRALSARG
RMAYMKDRVFGAADRIRMRLGRMAARPAADTQGLPPVLRQVRESMRVAMATYRPRRYLGS
PIVYVRASGREGGQGDPLPAWQRVARSGLLVKTIDGAHTDLVVEPNLAMVADTLARRLAG
A

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