Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_086511327.1 BZY95_RS18290 glutathione-disulfide reductase
Query= SwissProt::P85207 (461 letters) >NCBI__GCF_002151265.1:WP_086511327.1 Length = 453 Score = 222 bits (566), Expect = 2e-62 Identities = 150/445 (33%), Positives = 224/445 (50%), Gaps = 14/445 (3%) Query: 4 YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63 YDL VIG G GG AA A G +V E +GG C+NVGC+P K +AA + Sbjct: 6 YDLFVIGAGSGGVRAARTAAATGARVAVAEDRYLGGTCVNVGCVPKKLYSYAAHFHDAFE 65 Query: 64 GAEGFG--LKAKPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGPREIE 121 A GFG L P D L + +K+L LL VEL+ G AR +E Sbjct: 66 DARGFGWSLTEAPRFDWATLRDNKVREIKRLNEIYGRLLDNAGVELIHGRARVVDAHRVE 125 Query: 122 VNGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGAVGLEL 181 V+G + A ++A G P + FP E S +E +P+R LV+GGG + +E Sbjct: 126 VDGRAFSAAKILVAVGGWPW-VPDFPGRELTVTSNEVFDLER-MPRRFLVLGGGYIAVEF 183 Query: 182 GQIYHRLGSEVTLIEYMPEILPAG-DRETAALLRKALEKEGLKVRTGTKAVGYEKKQDGL 240 I++ LGSE L+ Y E+ G DRE R+ + +G+ + T EK + GL Sbjct: 184 ASIFNGLGSESHLV-YRGELFLRGFDREVREFTREQMALKGVNLHFETNIESIEKTEGGL 242 Query: 241 HVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAPG 300 V L + E + VD +L A GR+P EG+GL+ G+ ++ G ++VN R ET+ P Sbjct: 243 LVTLT-----NGESLEVDTVLAATGRKPHLEGVGLDALGIALNPDGTVKVNDRFETTTPS 297 Query: 301 VYAIGDVARPPLLAHKAMKEG--LVAAENAAGKNALFDFQ-VPSVVYTGPEWAGVGLTEE 357 + A+GDV P L A+ E LV+ D++ + + V+ P VGL+EE Sbjct: 298 ILALGDVTGGPELTPVALAEAMHLVSQHFGEAPPKPMDYRNIATAVFCHPNIGTVGLSEE 357 Query: 358 EARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEA 417 +ARK ++V + F L+ L+K++ D +D+++G +VG +AGELI Sbjct: 358 QARKEYDAIRVYRTDFRPMKHTLSGSEERCLMKLIVDDASDVVVGAHMVGEEAGELIQGI 417 Query: 418 TLALEMGATVSDLGLTIHPHPTLSE 442 +A++ G T +D T+ HPT +E Sbjct: 418 AIAVKAGLTKADFDATVGIHPTAAE 442 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: 527 Number of extensions: 32 Number of successful extensions: 5 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: 453 Length adjustment: 33 Effective length of query: 428 Effective length of database: 420 Effective search space: 179760 Effective search space used: 179760 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 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