Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_011779673.1 MVAN_RS12275 Si-specific NAD(P)(+) transhydrogenase
Query= SwissProt::P80647 (53 letters) >NCBI__GCF_000015305.1:WP_011779673.1 Length = 471 Score = 58.9 bits (141), Expect = 3e-14 Identities = 29/49 (59%), Positives = 33/49 (67%) Query: 5 EKDLVVIGSGPGGYVAAIKAAQLGMLTVCIEKYPTFGGTCLNVGCIPSK 53 E DLVVIGSGPGG AAI AA+LG +E+ GG C+N G IPSK Sbjct: 6 EYDLVVIGSGPGGQKAAIAAAKLGKTVAVVERGRMLGGVCVNTGTIPSK 54 Score = 20.8 bits (42), Expect = 0.009 Identities = 11/29 (37%), Positives = 15/29 (51%) Query: 8 LVVIGSGPGGYVAAIKAAQLGMLTVCIEK 36 +VV+G+G G A A LG +EK Sbjct: 181 MVVVGAGVIGIEYASMFAALGTKVTVVEK 209 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: 80 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 53 Length of database: 471 Length adjustment: 16 Effective length of query: 37 Effective length of database: 455 Effective search space: 16835 Effective search space used: 16835 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