Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_086511094.1 BZY95_RS17060 mercury(II) reductase
Query= SwissProt::P14218 (478 letters) >NCBI__GCF_002151265.1:WP_086511094.1 Length = 363 Score = 158 bits (399), Expect = 3e-43 Identities = 105/345 (30%), Positives = 169/345 (48%), Gaps = 8/345 (2%) Query: 115 VTSFEGHGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAP-LSDDIIVDSTG 173 +T G + + + V +G QV+ + +I +G+RP +PP P L+D + ST Sbjct: 7 ITVLHGEARFIDAHSLMVKLNEGGEQVVHFDRALIGTGARPA-VPPIPGLADTPYLTSTS 65 Query: 174 ALEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLT 233 AL +P++L VIGA V+ LEL +ARLG+ VTVL A + L D + Sbjct: 66 ALALDTLPERLIVIGASVVALELAQAFARLGSRVTVL-ARSRLLSQEDPAVGDAVEAAFR 124 Query: 234 KQGLNIRLGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGV 293 ++ + + + + + + V D N D+L+VA GR P T L A GV Sbjct: 125 RESIEVLKQTQASRVDYTDNEFIV---DTNAGTLRA-DQLLVATGRTPNTEALNLASLGV 180 Query: 294 TLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLI 353 RG I VD+H T+VPG++A GD + A+ G A + G +A ++ + Sbjct: 181 ET-ARGAILVDEHLHTTVPGLYAAGDCTDQPEFVYVAAAGGSRAAVNMTGGEATLDLSAM 239 Query: 354 PSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDR 413 P+VI+T P++A VG TE +G V+ RA+ DT G +K++A+ + R Sbjct: 240 PAVIFTDPQVATVGLTEAEAIEQGFSVDTRELDLENVPRALVNFDTGGFIKLVAERDSGR 299 Query: 414 VLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEAL 458 +LGV + A EL+Q + + + D+ +F + T+ E L Sbjct: 300 LLGVQAVAGEAGELIQTAVMALRARMTVHDIANELFPYLTMVEGL 344 Lambda K H 0.316 0.134 0.375 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: 359 Number of extensions: 23 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: 478 Length of database: 363 Length adjustment: 31 Effective length of query: 447 Effective length of database: 332 Effective search space: 148404 Effective search space used: 148404 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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