Align TPP-dependent acetoin dehydrogenase complex, E3 component, dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_005456519.1 SACCYDRAFT_RS12295 mercury(II) reductase
Query= CharProtDB::CH_006552 (578 letters) >NCBI__GCF_000244975.1:WP_005456519.1 Length = 471 Score = 236 bits (601), Expect = 2e-66 Identities = 146/465 (31%), Positives = 251/465 (53%), Gaps = 22/465 (4%) Query: 117 NLVVIGGGPGGYVAAIRAAQLGAKVTLIEKESLGGTCLNVGCIPTKVLLHSSQLLTEMKE 176 +L VIG G AA A + G V ++E+ + GGTCLNVGCIP+K +L ++ + Sbjct: 11 DLAVIGAGSAAKAAATEARRRGKSVAMVERAAPGGTCLNVGCIPSKNMLAAAAARASAQN 70 Query: 177 GDKLGI-----DIEGSIVVNWKHI---QKRKKIVIKKLVSGVSGLLTCNKVKVIKGTAKF 228 GI ++ S++V K ++R+K +K + +G++ +++GTA F Sbjct: 71 NRFPGILTSAGPVDLSLLVEAKDEFIRERREKDHVK--ATEQAGIV------LLRGTASF 122 Query: 229 ----ESKDTILVTKEDGVAEKVNFDNAIIATGSMPFIPEIEGNKLSGVIDSTGALSLESN 284 + + T++VT +G ++ ++ +IATG+ PFIP++ G + S A+SL+ Sbjct: 123 TPSGQERPTLMVTGPNGEETPISAEHVLIATGAQPFIPDVPGLADVDHLTSASAMSLDRV 182 Query: 285 PESIAIIGGGVIGVEFASIFNSLGCKVSIIEMLPHILPPMDREISEIAKAKLIRDGININ 344 PES+ ++GG IG+E A +F+ LG + +++E+ P I P D IS + L DGI+ Sbjct: 183 PESLLVVGGNAIGLEQAQLFSRLGARTTVVELAPRIAPFEDPSISATLQQALTDDGIDFL 242 Query: 345 NNCKVTRIEQGEDGLKVSFIGDKGEESIDVEKVLIAVGRRSNIEGLDVEKIGVKT-EGGS 403 +T ++ G+ + + I EK+L+A GRR +GL+++ +GV+ G Sbjct: 243 TGANLTGVQPTGTGVLATVTVGSDKLRIPTEKILVATGRRPATDGLNLDAVGVELGPRGE 302 Query: 404 IIVNDKMETNVEGIYAIGDCTGKIMLAHVASDQGVVAAENIMGQN-KKMDYKTVPACVYT 462 + V++ + T I+A GD TG+ +VA QGV A NI G + + +DY VP +T Sbjct: 303 VTVDEHLRTVHPRIWAAGDVTGQRQFVYVAGAQGVTAVSNIFGDSPRTLDYTAVPRVTFT 362 Query: 463 KPELASVGLTEEQAKEKGIDYKVGKFQLAANGKSLIMNETGGVIKIITDKKYEEILGVHI 522 P +ASVGLT + + Y+ + LA ++++ T G++K++++ ILGVH+ Sbjct: 363 SPAVASVGLTPHEVEATEQPYETRELPLAFVPRAMVSQRTNGLLKLVSEPGAGRILGVHM 422 Query: 523 LGPRATDLITEAALALRLEATLEEIITTVHAHPTVGEAMKEAALA 567 +G A ++IT A L T+E + T T+ E+++ AA A Sbjct: 423 VGEEAGEVITAATYLLSAGFTVERLAGTWAPFLTMAESLRIAAQA 467 Score = 25.0 bits (53), Expect = 0.007 Identities = 11/30 (36%), Positives = 20/30 (66%) Query: 116 DNLVVIGGGPGGYVAAIRAAQLGAKVTLIE 145 ++L+V+GG G A ++LGA+ T++E Sbjct: 184 ESLLVVGGNAIGLEQAQLFSRLGARTTVVE 213 Lambda K H 0.313 0.134 0.365 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: 517 Number of extensions: 15 Number of successful extensions: 5 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: 578 Length of database: 471 Length adjustment: 35 Effective length of query: 543 Effective length of database: 436 Effective search space: 236748 Effective search space used: 236748 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 52 (24.6 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