GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Shewanella sp. ANA-3

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 7022666 Shewana3_4311 putative mercuric reductase (RefSeq)

Query= SwissProt::P80647
         (53 letters)



>FitnessBrowser__ANA3:7022666
          Length = 551

 Score = 51.2 bits (121), Expect = 7e-12
 Identities = 23/52 (44%), Positives = 32/52 (61%)

Query: 2   SSGEKDLVVIGSGPGGYVAAIKAAQLGMLTVCIEKYPTFGGTCLNVGCIPSK 53
           S+  + + +IG+G G +  AIKAA+ G     IE     GG C+NVGC+PSK
Sbjct: 85  SNRTQHVAIIGTGSGAFACAIKAAEGGAKVTLIEGADVIGGCCVNVGCVPSK 136


Lambda     K      H
   0.319    0.140    0.428 

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: 88
Number of extensions: 4
Number of successful extensions: 1
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: 53
Length of database: 551
Length adjustment: 17
Effective length of query: 36
Effective length of database: 534
Effective search space:    19224
Effective search space used:    19224
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 (21.7 bits)
S2: 43 (21.2 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