GapMind for catabolism of small carbon sources

 

Protein GFF2604 in Pseudomonas stutzeri RCH2

Annotation: Psest_2654 fatty oxidation complex, alpha subunit FadB

Length: 715 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 26 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism fadB hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
4-hydroxybenzoate catabolism paaH hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
L-arginine catabolism fadB hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
L-citrulline catabolism fadB hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
L-isoleucine catabolism ech hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
L-lysine catabolism fadB hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
phenylacetate catabolism fadB hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
phenylacetate catabolism paaH hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
L-phenylalanine catabolism fadB hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
L-phenylalanine catabolism paaH hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
L-proline catabolism fadB hi fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized) 89% 100% 1261.1
4-hydroxybenzoate catabolism ech med crotonase (EC 4.2.1.150) (characterized) 44% 71% 137.9
L-arginine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 44% 71% 137.9
L-citrulline catabolism ech med crotonase (EC 4.2.1.150) (characterized) 44% 71% 137.9
L-lysine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 44% 71% 137.9
phenylacetate catabolism ech med crotonase (EC 4.2.1.150) (characterized) 44% 71% 137.9
L-phenylalanine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 44% 71% 137.9
L-proline catabolism ech med crotonase (EC 4.2.1.150) (characterized) 44% 71% 137.9
L-valine catabolism ech med crotonase (EC 4.2.1.150) (characterized) 44% 71% 137.9
4-hydroxybenzoate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 33% 98% 360.1 fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) 89% 1261.1
phenylacetate catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 33% 98% 360.1 fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) 89% 1261.1
L-phenylalanine catabolism pimF lo 6-carboxyhex-2-enoyl-CoA hydratase (characterized) 33% 98% 360.1 fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) 89% 1261.1
L-isoleucine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 33% 86% 120.6 fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) 89% 1261.1
propionate catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 33% 86% 120.6 fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) 89% 1261.1
L-threonine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 33% 86% 120.6 fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) 89% 1261.1
L-valine catabolism hpcD lo 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) 33% 86% 120.6 fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) 89% 1261.1

Sequence Analysis Tools

View GFF2604 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

MIYEGKAITVKALESGIVELNFDLKGESVNKFNRLTLNDLRQAVDAIKADASVKGVIVTS
GKDVFIVGADITEFVDNFKMADEELVAGNLEANKIFSDFEDLGVPTVAAINGIALGGGFE
MCMAADYRVMSTTAKVGLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDAL
KVHAVDAVVAPDKLQAAALDLVKRAISGELDYKAKRQPKLDKLKLNAIEQMMAFETSKAF
VAGQAGPNYPAPVEAIKTIQKAANFTRDKAIEVEAAGFVKLAKTSVAQSLVGLFLSDQEL
KKKAKAYDKQARDVKLAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEGIQMGLDEASKL
LGKRVEKGRLTADKMAQALNAIRPTMSYGDFGNVDIVVEAVVENPKVKHAVLAEVEGHVR
EDAIIASNTSTISINYLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTSEVAIATTVA
YAKKMGKSPVVVNDCPGFLVNRVLFPYFGGFARAIAHGVDFVRADKVMEKFGWPMGPAYL
MDVVGMDTGHHGRDVMAEGFPDRMKDDTRTAVDVMYEANRLGQKNGKGFYAYEMDKKGKP
KKVVDAQAYELLKPIVAETRELSDEDIINYMMIPLCLETVRCLEDGIVETAAEADMGLIY
GIGFPPFRGGALRYIDSIGVAEFVAMADKYADLGPLYHPTAKLREMAANGQRFYG

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