GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Magnetospirillum magneticum AMB-1

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_011384506.1 AMB_RS10625 3-oxoacyl-[acyl-carrier-protein] reductase

Query= BRENDA::Q4J9F2
         (255 letters)



>NCBI__GCF_000009985.1:WP_011384506.1
          Length = 245

 Score =  118 bits (296), Expect = 1e-31
 Identities = 83/253 (32%), Positives = 129/253 (50%), Gaps = 14/253 (5%)

Query: 6   LKNKVVIVTGAGSGIGRAIAKKFALNDSIVVAVELLEDRLNQIVQELRGMGKEVLGVKAD 65
           L  K  +VTGA  GIG AIAK      + V       + L+ +  EL   G+ V  + A+
Sbjct: 4   LTGKTALVTGASGGIGGAIAKALHARGATVGLHGTRREALDALAAEL---GERVHVLPAN 60

Query: 66  VSKKKDVEEFVRRTFETYSRIDVLCNNAGIM-DGVTPVAEVSDELWERVLAVNLYSAFYS 124
           +S    VE+  +        +D+L NNAG+  DG+  V  + DE W+ VL VNL +AF  
Sbjct: 61  LSDAAAVEQLAKDAEAAMGSVDILVNNAGLTKDGL--VLRMKDEDWQTVLDVNLTAAFRL 118

Query: 125 SRAVIPIMLKQGKGVIVNTASIAGIRGGFAGAPYTVAKHGLIGLTRSIAAHYGDQGIRAV 184
           SRA +   +K+  G I+N  SI G+ G      Y  +K G+IG+++++A     + I   
Sbjct: 119 SRAAVKGQMKRRWGRIINITSIVGVTGNPGQVNYAASKAGMIGMSKALAQEVASRNITVN 178

Query: 185 AVLPGTVKTNIGLGSSKPSELGMRTLTKLMS--LSSRLAEPEDIANVIVFLASDEASFVN 242
            V PG V       S+    L     TKL +   + R+   ++IA  +V+LAS EA++V 
Sbjct: 179 CVAPGFV------SSAMTDVLSDEQKTKLNAGIPAGRMGTADEIAAAVVYLASAEAAYVT 232

Query: 243 GDAVVVDGGLTVL 255
           G  + V+GG+ ++
Sbjct: 233 GQTLHVNGGMAMI 245


Lambda     K      H
   0.318    0.135    0.369 

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: 138
Number of extensions: 8
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: 255
Length of database: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

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 (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:

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. 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:

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:

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