Alignments for a candidate for adh in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Methylobacterium nodulans ORS 2060

Align aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) (characterized)
to candidate WP_015926996.1 MNOD_RS01175 aldehyde dehydrogenase family protein

Query= BRENDA::Q69P84
         (509 letters)



>NCBI__GCF_000022085.1:WP_015926996.1
          Length = 509

 Score =  460 bits (1184), Expect = e-134
 Identities = 244/477 (51%), Positives = 312/477 (65%), Gaps = 5/477 (1%)

Query: 37  VTSTNPTNNQVIAEVVEASAREYEEGMRACYDAAKTWMAIPAPKRGEIVRQIGDALRAKL 96
           V + +P +   I  + E +  E E  +    +    W  +PAP+RGE+VR +G+ LRA  
Sbjct: 31  VPARSPIDGLTIGHLHETTDAEAEAAIGRAAEVFLAWRRVPAPRRGELVRLLGEELRAAK 90

Query: 97  HHLGRLVSLEMGKILPEGIGEVQEIIDMCDYAVGLSRQLNGSIIPSERPNHMMMEVWNPL 156
             LGRLV LE GKIL EG+GEVQE+ID+CD+AVGLSRQL+G  I +ERP+H MMEVW+PL
Sbjct: 91  ADLGRLVMLETGKILSEGLGEVQEMIDICDFAVGLSRQLHGLTIATERPDHRMMEVWHPL 150

Query: 157 GVVGVITAFNFPCAVLGWNACIALVCGNCVVWKGAPTTPLITIAMTKIVASVLER--NNL 214
           G  GVITAFNFP AV  WNA +ALVCG+ V+WK +  TPL  +A+  I    L+R     
Sbjct: 151 GPCGVITAFNFPVAVWSWNAALALVCGDPVLWKPSEKTPLTALAVQAIAGRALKRFGAEA 210

Query: 215 PGSIFTAFCGGADIGQAISLDTRIPLVSFTGSTKVGLMVQQQVNARFGKCLLELSGNNAI 274
           P  +     GG  +G+ ++ D RIPLVS TGST +G  V   + ARF + +LEL GNNA 
Sbjct: 211 PEGLLQVLIGGRSLGERLAADPRIPLVSATGSTAMGRQVAPVLAARFARAILELGGNNAA 270

Query: 275 IVMDDADIQLAVRSVLFAAVGTAGQRCTTCRRLLLHESIYRTFLDQLVEVYKQVRIGDPL 334
           IV   AD+ LA+R+V FAA+GTAGQRCTT RRL + ESIY  FL +L   Y  VRIGDP 
Sbjct: 271 IVAASADLDLALRAVAFAAMGTAGQRCTTLRRLFVQESIYDAFLPRLRTAYASVRIGDPR 330

Query: 335 ENGTLLGPLHTPASRDAFLKGIQTIRSQGGKILYGGSAIESEGN---FVQPTIVEISPSA 391
           +  TL+GPL   ++ D   + +   R+ G  I  G    +  G+   +++P +VE+   A
Sbjct: 331 DPATLVGPLIDLSAADGMARALDEARALGATIQGGERLSDIRGDAAAYLRPALVEMRTQA 390

Query: 392 PVVREELFGPVLYVMKVQNLKEAVEINNSVPQGLSSSIFTKRPDIIFKWIGPHGSDCGIV 451
             +  E F P+LYV+  + L EA+   N+V  GLSSSIFT+       ++   GSDCGI 
Sbjct: 391 GPMLRETFAPILYVVPYRELDEAIAAQNAVAAGLSSSIFTRDLSEAEIFLSVAGSDCGIA 450

Query: 452 NVNIPTNGAEIGGAFGGEKATGGGREAGSDSWKQYMRRATCTINYGSELPLAQGINF 508
           NVNI  +GAEIGGAFGGEKATGGGREAGSDSWK YMRRAT TINYG  LPLAQG++F
Sbjct: 451 NVNIGPSGAEIGGAFGGEKATGGGREAGSDSWKAYMRRATNTINYGKSLPLAQGVSF 507


Lambda     K      H
   0.320    0.137    0.416 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 691
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 509
Length of database: 509
Length adjustment: 34
Effective length of query: 475
Effective length of database: 475
Effective search space:   225625
Effective search space used:   225625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 (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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources