GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Snodgrassella alvi wkB2

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_025331338.1 SALWKB2_RS08960 3-oxoacyl-ACP reductase FabG

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_000600005.1:WP_025331338.1
          Length = 247

 Score =  123 bits (309), Expect = 3e-33
 Identities = 79/251 (31%), Positives = 124/251 (49%), Gaps = 19/251 (7%)

Query: 8   LAGKTVLITAAAQGIGRASTELFAREGARVIATDISK---THLEELASIAGVETHLLDVT 64
           L GK  L+T A +GIG A     A +GA+VI T  S    T + E  +  G E   L + 
Sbjct: 5   LTGKIALVTGATRGIGAAIARFLAEKGAKVIGTATSAAGVTSINEALADFGGEGRELRIA 64

Query: 65  DDDAIKALVA----KVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAV 120
           ++++I+ L+A     +G + +L N AG      ++   +  WD    +N K+ F   +AV
Sbjct: 65  EENSIENLIADIESNIGNIAILVNNAGITRDNLLMRMKESEWDEIMQINLKSAFRASKAV 124

Query: 121 LPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAIC 180
              M+  + G I+N+ S    + G A +  Y A+KA +VG +KS+A +  S+GI  N + 
Sbjct: 125 TRSMMKARWGRIINVTSVVGFI-GNAGQANYAAAKAGLVGFSKSMAREVGSRGITVNCVA 183

Query: 181 PGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNF 240
           PG IE+             T     E R  F  +  +   G  E+VAA  L+LAS+E+ +
Sbjct: 184 PGFIETDM-----------TKVLPQEQRDFFAGQTALNHFGTVEDVAAAVLFLASEEARY 232

Query: 241 TTGSIHMIDGG 251
            TG    ++GG
Sbjct: 233 ITGQTLHVNGG 243


Lambda     K      H
   0.316    0.129    0.359 

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: 142
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: 254
Length of database: 247
Length adjustment: 24
Effective length of query: 230
Effective length of database: 223
Effective search space:    51290
Effective search space used:    51290
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 24 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