GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Nocardiopsis gilva YIM 90087

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_017617176.1 CDO52_RS11130 3-oxoacyl-ACP reductase

Query= SwissProt::Q92EU6
         (254 letters)



>NCBI__GCF_002263495.1:WP_017617176.1
          Length = 254

 Score =  143 bits (360), Expect = 4e-39
 Identities = 87/241 (36%), Positives = 137/241 (56%), Gaps = 7/241 (2%)

Query: 15  KVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVDITKKEN 74
           +VAV+TGA SGIGKA A   + +G  VV +D+  D  +  A+   +  L +  D+T +E 
Sbjct: 7   RVAVITGAGSGIGKATALRLASEGGTVVAVDLDRDAGEAVAK--ETGGLYIAADVTDEEA 64

Query: 75  IEKVVAEIKKVYPKIDILANSAGVALLEKAE--DLPEEYWDKTMELNLKGSFLMAQIIGR 132
           ++   AE+K+VY ++D+  N+AG++  +     D   E W K  E+NL   +L  +    
Sbjct: 65  VKAAFAEVKEVYGRVDVAFNNAGISPPDDDSILDTGIEAWRKVQEVNLTSVYLCCKYALP 124

Query: 133 EMIATGGGKIVNMAS-QASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAISPT 191
            M   G G IVN AS  A++ A    ++Y ASK  +++M++ L +++A   + VNA+SP 
Sbjct: 125 YMREQGKGAIVNTASFVATMGAATSQISYTASKGGVLAMSRELGVQFARDGVRVNALSPG 184

Query: 192 VILTELGKKAWAGQVGEDMKKLI--PAGRFGYPEEVAACALFLVSDAASLITGENLIIDG 249
            + T L K+ +A       ++L+  P GRF  PEE+A+   FL SD AS IT  N ++DG
Sbjct: 185 PVNTPLLKELFAKDPERAQRRLVHVPFGRFAEPEEIASAVAFLASDDASFITASNFLVDG 244

Query: 250 G 250
           G
Sbjct: 245 G 245


Lambda     K      H
   0.316    0.133    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: 160
Number of extensions: 9
Number of successful extensions: 5
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: 254
Length adjustment: 24
Effective length of query: 230
Effective length of database: 230
Effective search space:    52900
Effective search space used:    52900
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 (21.6 bits)
S2: 47 (22.7 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