Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate SM_b21143 SM_b21143 mercuric reductase
Query= SwissProt::P85207 (461 letters) >FitnessBrowser__Smeli:SM_b21143 Length = 473 Score = 238 bits (606), Expect = 4e-67 Identities = 141/446 (31%), Positives = 231/446 (51%), Gaps = 8/446 (1%) Query: 2 KTYDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHH 61 K +D ++IG G G A R + +G V +E GG C+N GC+PTKA++ +A +H Sbjct: 19 KHFDAVIIGAGQAGPSLAGRLSGVGKTVALIERKLFGGTCVNTGCMPTKAMVASAYAIHT 78 Query: 62 LKGAEGFGLKAKP-ELDLKKLGAWRDGVVKKLTGGVAGLLKGNK-VELLRGFARFKGPRE 119 + +G+ P +D ++ A ++ V GV LKG K + G ARF+GPRE Sbjct: 79 ARRGAEYGMTTGPVSVDFGRVMARKEKVRLDARSGVEKWLKGMKNCTVFEGHARFEGPRE 138 Query: 120 IEVNGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEG-IPKRLLVIGGGAVG 178 + + E + + G + P DV T + ++ +P+ L+V+GG +G Sbjct: 139 VRIGDELISGERIFVNVGGRAA-VADLPGVNDVPYLTNSSIMDLAELPEHLVVVGGSYIG 197 Query: 179 LELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQD 238 LE Q++ R GS+VT+IE ++ D E + +R+ LE EG+++RT + + + D Sbjct: 198 LEFAQMFRRFGSDVTVIEKGARLIGREDPEVSDAIREILENEGVRIRTNAECIRFSNHAD 257 Query: 239 GLHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSA 298 + V ++ G + E+ +L+A GR P T+ LGL+KAGVK DERG+I+V+ + T+ Sbjct: 258 SVAVGVDCTSG--EPEVSGSHVLLATGRHPNTDDLGLDKAGVKTDERGYIEVDDSLRTNV 315 Query: 299 PGVYAIGDVARPPLLAHKAMKEGLVAAENAAGKNA--LFDFQVPSVVYTGPEWAGVGLTE 356 P ++A+GD H + + + A N + + D +Y P G+TE Sbjct: 316 PHIFAMGDCNGRGAFTHTSYNDFEIVAANLIDNDPRRVSDRIQTYALYIDPPLGRAGMTE 375 Query: 357 EEARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAE 416 EARK G+ + VG P + GRA+ G +G +KV+ DAETD +LG ++G E + Sbjct: 376 TEARKKGHKLLVGTRPMTRVGRAVEKGETQGFMKVIVDAETDEILGASILGTGGDEAVQS 435 Query: 417 ATLALEMGATVSDLGLTIHPHPTLSE 442 + + + +H HPT+SE Sbjct: 436 ILDVMYAKKPYTMIARAVHIHPTVSE 461 Lambda K H 0.316 0.138 0.395 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: 583 Number of extensions: 35 Number of successful extensions: 6 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: 461 Length of database: 473 Length adjustment: 33 Effective length of query: 428 Effective length of database: 440 Effective search space: 188320 Effective search space used: 188320 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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