Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_057507276.1 ABB28_RS03090 mercuric reductase
Query= SwissProt::P85207 (461 letters) >NCBI__GCF_001431535.1:WP_057507276.1 Length = 466 Score = 224 bits (572), Expect = 4e-63 Identities = 151/444 (34%), Positives = 226/444 (50%), Gaps = 8/444 (1%) Query: 4 YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63 +D I+IG G G A R G +V +E VGG C+N GC PTK L+ +A VH + Sbjct: 11 FDAIIIGAGQAGPSLAGRLNAAGKRVAIIERHLVGGTCVNTGCKPTKTLVASAYAVHTAR 70 Query: 64 GAEGFGLKA-KPELDLKKLGAWRDGVVKKLTGGVAGLLKGN-KVELLRGFARFKGPREIE 121 +G + ++D+ + A V+ G L G VEL+RG ARF G + +E Sbjct: 71 RGGEYGFSTGEVDVDMPAVAARARQVIDDSRGSNEAWLDGMLNVELIRGHARFIGSKLVE 130 Query: 122 VNGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVE-EGIPKRLLVIGGGAVGLE 180 VNG+ A + I G P + P +V T A V + +P+ L+VIGG +GLE Sbjct: 131 VNGQHLTAPNIFINVGGRP-GIPDLPGLMNVPFMTNAGMVALDVLPRHLIVIGGSYIGLE 189 Query: 181 LGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQDGL 240 Q+Y R G+EVTLIE ++P D + +A +R+ LE E +KV T + + Sbjct: 190 FAQMYRRFGAEVTLIERSDRLIPREDPDISAAVRRILEGEHIKVLTSASRIEFRSDGQDT 249 Query: 241 HVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAPG 300 +LLE G + IV +LVA GR P T+ LGL+ AG+ DE G+I+V+ R++T+ G Sbjct: 250 TILLETEAGPTA--IVGSHVLVATGRVPNTDALGLDAAGIACDEHGYIRVDERLQTTVDG 307 Query: 301 VYAIGDVARPPLLAHKAMKE-GLVAAENAAGKNALFDFQVPS-VVYTGPEWAGVGLTEEE 358 VYA+GD H A + +VAA G + +V S ++ P A VGLT+ + Sbjct: 308 VYALGDCNGQGTFTHTAYNDFEIVAANLLDGDDRHVSSRVSSYALFIDPPLARVGLTQAQ 367 Query: 359 ARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEAT 418 A G + K + GRA+ G +G + V+ DAET +LG ++G E I Sbjct: 368 AVATGRPLLYSKREMTRVGRAVEKGETKGFMTVIADAETRQVLGAAILGTGGDEAIHGLL 427 Query: 419 LALEMGATVSDLGLTIHPHPTLSE 442 + T+ ++ + HPT++E Sbjct: 428 NMMNAERTIDEIRWAVPIHPTVAE 451 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: 538 Number of extensions: 30 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: 466 Length adjustment: 33 Effective length of query: 428 Effective length of database: 433 Effective search space: 185324 Effective search space used: 185324 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 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