GapMind for catabolism of small carbon sources

 

Protein 8501604 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_2322 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)

Length: 904 amino acids

Source: Miya in FitnessBrowser

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism ald-dh-CoA hi alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized) 59% 93% 1049.3
2'-deoxyinosine catabolism ald-dh-CoA hi alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized) 59% 93% 1049.3
2-deoxy-D-ribose catabolism ald-dh-CoA hi alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized) 59% 93% 1049.3
ethanol catabolism ald-dh-CoA hi alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized) 59% 93% 1049.3
ethanol catabolism etoh-dh-nad hi alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized) 59% 93% 1049.3 aldehyde dehydrogenase/alcohol dehydrogenase (EC 1.2.1.57) 56% 998.0
L-threonine catabolism ald-dh-CoA hi alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized) 59% 93% 1049.3
thymidine catabolism ald-dh-CoA hi alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized) 59% 93% 1049.3
L-tryptophan catabolism ald-dh-CoA hi alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized) 59% 93% 1049.3
4-hydroxybenzoate catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 99% 966.1 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
2'-deoxyinosine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 99% 966.1 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
2-deoxy-D-ribose catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 99% 966.1 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
ethanol catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 99% 966.1 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
L-threonine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 99% 966.1 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
thymidine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 99% 966.1 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
L-tryptophan catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 99% 966.1 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized) 38% 96% 305.4 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized) 38% 96% 305.4 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized) 38% 96% 305.4 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
L-fucose catabolism fucO lo Lactaldehyde reductase (characterized, see rationale) 37% 97% 238.4 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3
L-rhamnose catabolism fucO lo Lactaldehyde reductase (characterized, see rationale) 37% 97% 238.4 alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) 59% 1049.3

Sequence Analysis Tools

View 8501604 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSKKPNAQGAKPATTPDAISLNDISPSSIAPNSITVDDIVTRVNEAQRAFANFTQQQVDA
IFHAAAAAATAQRIHLARMAVQETGMGILEDKVIKNHFASEYIYNKYKDDKTCGVIRDDP
AYGYREVAAPIGVIAGIIPTTNPTSTTIFKALLALKTRNGIIFAPHPRAAKSTVEAARIV
HEAAVAAGAPRGIIGWVEAPTPDLTRQLMQHRGVALILATGGPGMVHAAYSSGKPAIGVG
AGNTPVVVDASANVKMAVNSIILSKTFDNGMICASEQAVIVEDAAADAVKAEFAARGCHF
ASPQEAEALAGVVFTDGRLNAAIVGRSAAEIAAMAGITVPPTTKILIAERDAIDPLDPFA
HEKLSPVLGFYRAPDFAAAVDMAQRLVELGGAGHTSVLYTNEANRERIVHFQNVLTTGRT
LVNMPSSQGAIGDVYNFELAPSLTLGCGSWGDNSVSENIGVKHLMNVKTVAERRENMLWF
RVPPKIYFKMGALRLALEDMRDRKRAFIVTDRTMEDLGHVGKVTAVLEKLGIQFRVFSDV
KPDPDLSGTYAALDSIRAFRPDMFIALGGGSPMDAAKIMWLMYEQPDLKFEEISLRFMDI
RKRVHAFPALGKKAVMVAVPTTSGTGSEVTPFAVITDDATGMKYPIADYELTPDMAIVDP
EFVMDMPKTLTAHSGLDALTHAVEAFTSTYANNFSDGNALEAVRLVFKYLRRAYNDGARD
VMAREKMHYAGTIAGMAFANAFLGVCHSMAHKLGAAFHMPHGLANALLLSHVIEYNATDT
PTKQGLMPQYRYPFVKGRYARIADMLGLTEGCGDDRDRKVARLVQAIEQLKADLNVPGSL
REAGIAEADFLERVDLLAEQAFDDQCTGGNPRYPLIAEIRELYLKAYYGAPLASLASPPP
AKAG

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, 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