Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_046009069.1 OLEAN_RS09670 glutathione-disulfide reductase
Query= CharProtDB::CH_004665 (470 letters) >NCBI__GCF_000967895.1:WP_046009069.1 Length = 460 Score = 231 bits (588), Expect = 5e-65 Identities = 147/453 (32%), Positives = 228/453 (50%), Gaps = 10/453 (2%) Query: 11 DTLVIGAGPGGYVAAIRAAQLGQKVTVVEKATLGGVCLNVGCIPSKALINAGHRYENAKH 70 D +VIGAG GG +A AA G+KV ++E LGG C+NVGC+P K + A E + Sbjct: 9 DLVVIGAGSGGVRSARMAAAQGKKVAIIENRYLGGTCVNVGCVPKKMFVYASEYREKMEE 68 Query: 71 SDDMGITAENVTVDFTKVQEWKASVVNKLTGGVAGLLKGNKVDVVKGEAYFVDSNSVRVM 130 + GI + + +++ K++ + +L G A LL G + G +D+N+V V Sbjct: 69 AKGFGINGQVNDFHWPTLRDNKSNEIARLNGIYANLLTGPGATIFNGTGSLIDANTVHVN 128 Query: 131 -DENSAQTYTFKNAIIATGSRPIELPNFKYSERVLNSTGALALK--EIPKKLVVIGGGYI 187 + S Q T +IATGS P + P +E + S +L+ E P + +V+G GYI Sbjct: 129 GQDGSQQDVTADTILIATGSWPFK-PEVPGAEHAITSNEVFSLEDDEFPLRALVVGAGYI 187 Query: 188 GTELGTAYANFGTELVILEGGDEILPGFEKQMSSLVTRRLKKKGNVEIHTNAMAKGVEER 247 E + GTE + D +L GF+ + + V ++ +KG V I +E++ Sbjct: 188 AVEFAGIFNGLGTETTLALRKDLVLRGFDDDIRAFVQGQMIEKG-VNILPETEVDHIEKQ 246 Query: 248 PDGVTVTFEVKGEEKTVDADYVLITVGRRPNTDELGLEQVGIEMTDRGIVKTDKQCRTNV 307 DG + F E++ + D VL GRRP TD L LE++GI++ +K D +T+V Sbjct: 247 ADGSLMVFYTNNEQQ--EFDLVLYATGRRPMTDGLNLEKLGIDLNSDTTIKVDDFFQTSV 304 Query: 308 PNIYAIGDIIEGPPLAHKASYEG-KIAAEAIAGEPAEIDYLGIPAVVFSEPELASVGYTE 366 P++YA+GD+I P L A +G K A + ++Y IP VF +P + +VG TE Sbjct: 305 PSVYALGDVIGTPQLTPVALAQGMKFLAHQYHDDTVPMNYDNIPTAVFCQPNIGTVGPTE 364 Query: 367 AQAKEEGLDIVAAKFPFAANGRALSLNETDGFMKLITRKEDGLVIGAQIAGASASDMISE 426 + K +G++ + F +S MKLI K + VI A + G A + I Sbjct: 365 DECKAQGIEFDVYESNFKPLKHTISGMNERTLMKLIVNKANNKVIAAHMVGHDAGETIQG 424 Query: 427 LSLAIEGGMTAEDIAMTIHAHPTLGE--ITMEA 457 +++AI G T D TI HPT E +TM + Sbjct: 425 IAVAITAGATKADFDATIGIHPTSAEEFVTMRS 457 Lambda K H 0.314 0.134 0.372 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: 509 Number of extensions: 27 Number of successful extensions: 4 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: 460 Length adjustment: 33 Effective length of query: 437 Effective length of database: 427 Effective search space: 186599 Effective search space used: 186599 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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