Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_011655126.1 RL_RS31705 FAD-containing oxidoreductase
Query= SwissProt::P85207 (461 letters) >NCBI__GCF_000009265.1:WP_011655126.1 Length = 453 Score = 253 bits (645), Expect = 1e-71 Identities = 149/448 (33%), Positives = 240/448 (53%), Gaps = 13/448 (2%) Query: 1 MKTYDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVH 60 MK++D IVIG G G A R + G+KV +E +GG C+N GC+PTK L+ +A H Sbjct: 1 MKSFDAIVIGAGQAGPFLAARMVEKGMKVALIERKFLGGTCVNAGCMPTKTLVASARAAH 60 Query: 61 HLKGAEGFGLKAKPEL--DLKKLGAWRDGVVKKLTGGVAGLLKG-NKVELLRGFARFKGP 117 + + +G+ E+ D+ + A + V G+ G G + + ++ G ARF+GP Sbjct: 61 VARNSAAYGVNIPGEIAIDMTVVRARAETVTMNARNGLIGWFAGMDGMTVIYGHARFEGP 120 Query: 118 REIEVNGETYGAQSFIIATGSEPM-PLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGA 176 + + VNGET A + G+ P+ P D ST + ++ +P+ L+VIGG Sbjct: 121 KTVSVNGETLTAPRIFLNVGARPVIPELSGVNDIDYLTSTSIIHLDT-LPRHLVVIGGSY 179 Query: 177 VGLELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKK 236 +GLE Q+Y R G+EV++IE+ P++ D + + + L EG+ + TG + + K Sbjct: 180 IGLEFAQMYRRFGAEVSVIEHGPKLASREDEDISDAIADVLRSEGIDIHTGVSDIAFAKS 239 Query: 237 QDGLHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMET 296 DG+ V ++A+ I +L+A GR+P T+ LGL+ AGV D RGFI V+ R+ T Sbjct: 240 SDGITVATDSAR------IDASHVLIATGRKPNTDDLGLDAAGVITDGRGFITVDDRLAT 293 Query: 297 SAPGVYAIGDVARPPLLAHKAMKEGLVAAENAA-GKNALFDFQVPS-VVYTGPEWAGVGL 354 + G++A+GD H + + +AA N G + ++P+ +Y P VG+ Sbjct: 294 NVDGIWALGDCNGHGAFTHTSYNDFEIAAANLLDGDDRKVSSRIPAYALYIDPPLGRVGM 353 Query: 355 TEEEARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELI 414 TE++AR +G + + P S GRA G +G +KV+ DAET +LG ++G + E+I Sbjct: 354 TEKQARASGRKIMISTRPMSRVGRANERGETKGFMKVIADAETKKILGAAILGIEGDEVI 413 Query: 415 AEATLALEMGATVSDLGLTIHPHPTLSE 442 A+ G T L ++ HPT+SE Sbjct: 414 HGIIDAMNAGTTYPALQWSVPIHPTVSE 441 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: 491 Number of extensions: 24 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 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