Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_086508722.1 BZY95_RS04225 Si-specific NAD(P)(+) transhydrogenase
Query= SwissProt::P80647 (53 letters) >NCBI__GCF_002151265.1:WP_086508722.1 Length = 463 Score = 52.0 bits (123), Expect = 4e-12 Identities = 25/47 (53%), Positives = 30/47 (63%) Query: 7 DLVVIGSGPGGYVAAIKAAQLGMLTVCIEKYPTFGGTCLNVGCIPSK 53 D+VVIG+GP G AAI AA+ G +EK P GG C + G IPSK Sbjct: 7 DVVVIGTGPAGESAAINAAKHGKRVAVVEKQPVLGGNCTHWGTIPSK 53 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: 67 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: 463 Length adjustment: 16 Effective length of query: 37 Effective length of database: 447 Effective search space: 16539 Effective search space used: 16539 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: 42 (20.8 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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