Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate WP_057687275.1 ABB28_RS15505 glutathione-disulfide reductase
Query= SwissProt::P11959 (470 letters) >NCBI__GCF_001431535.1:WP_057687275.1 Length = 455 Score = 199 bits (505), Expect = 2e-55 Identities = 141/454 (31%), Positives = 221/454 (48%), Gaps = 19/454 (4%) Query: 7 AIETETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYE 66 A + + +V+G G GG AA RAAQ G+KV ++E G LGG C+NVGC+P KA+ A+ Sbjct: 5 AHDYDLIVLGGGSGGLAAAFRAAQHGRKVAMLEPGELGGTCVNVGCVPKKAMWLAADLAG 64 Query: 67 QAKHSEEMGIKAENVTIDFAKVQEWKASVVKKLTGGVEGL-------LKGNKVEIVKGEA 119 + + MG + WK VV + G +E + L V V Sbjct: 65 RIGLARAMGF-----DVPLRPALSWKELVVHR-QGYIENIHVSYRKRLDETGVVRVPRRG 118 Query: 120 YFVDANTVRVVNGDSAQTYTFKNAIIATGSRPIELPNFKFSNRILDSTGALNLGEVPKSL 179 VDA+TV +G + ++ ++ATG+ P + P+ + L S NL + P + Sbjct: 119 RLVDAHTVECSDG---VRISGEHILLATGAHP-QRPDIPGAELGLVSDDFFNLCDAPAQV 174 Query: 180 VVIGGGYIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNAL 239 ++GGGYI +EL G++VT+L G +L F+ ++AA + L +GV + N Sbjct: 175 AIVGGGYIAVELAGLLQALGSRVTLLVRGGRLLDRFDGELAAQLADNLCHQGVRIHFNYR 234 Query: 240 AKGAEEREDGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVD 299 + + +DG V + D V +GRR N+ ++GLEQ+G+ + RG + VD Sbjct: 235 LRELQRDDDGQRVRVLGHDGPLDSVFDTVFFAIGRRGNSSDIGLEQVGVAVGERGEVIVD 294 Query: 300 QQCRTSVPNIFAIGDIVPGPALAHKASYEGKVAAEAI-AGHPSA-VDYVAIPAVVFSDPE 357 + TSVP+I A+GDI L A + + + G P A +DY +P+VVFS P Sbjct: 295 EWQDTSVPSIHAVGDIGGKVGLTPVAIAAARHLMDRLFGGKPDAKMDYANVPSVVFSHPP 354 Query: 358 CASVGYFEQQAKDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGP 417 VG E++A+ + DV F +ALA KLV D ++G ++G Sbjct: 355 LGMVGLGEEEARAQHGDVRTYHSNFRPMLQALADGTQRSMFKLVCVGADERVVGVHLLGE 414 Query: 418 NASDMIAELGLAIEAGMTAEDIALTIHAHPTLGE 451 A +++ +A++ G T T+ HPT E Sbjct: 415 AADEILQGFAVAVKMGATKAQFDDTVAIHPTSSE 448 Lambda K H 0.316 0.135 0.376 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: 548 Number of extensions: 33 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: 470 Length of database: 455 Length adjustment: 33 Effective length of query: 437 Effective length of database: 422 Effective search space: 184414 Effective search space used: 184414 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