Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate BWI76_RS26685 BWI76_RS26685 glutathione-disulfide reductase
Query= CharProtDB::CH_004665 (470 letters) >FitnessBrowser__Koxy:BWI76_RS26685 Length = 450 Score = 216 bits (551), Expect = 1e-60 Identities = 143/448 (31%), Positives = 225/448 (50%), Gaps = 15/448 (3%) Query: 11 DTLVIGAGPGGYVAAIRAAQLGQKVTVVEKATLGGVCLNVGCIPSKALINAGHRYENAK- 69 D + IG G GG + RAA GQK ++E LGG C+NVGC+P K + +A E Sbjct: 6 DYIAIGGGSGGIASINRAAMHGQKCALIEAKDLGGTCVNVGCVPKKVMWHAAQIREAIHL 65 Query: 70 HSDDMGITAENVTVDFTKVQEWKASVVNKLTGGVAGLLKGNKVDVVKGEAYFVDSNSVRV 129 + D G D+ K+ +++ ++++ +L NKVDV+KG A FVD+ ++ V Sbjct: 66 YGPDYGFDTTINHFDWDKLVASRSAYIDRIHTSYDNVLGKNKVDVIKGFARFVDAKTIEV 125 Query: 130 MDENSAQTYTFKNAIIATGSRPIELPNFKYSERVLNSTGALALKEIPKKLVVIGGGYIGT 189 + +T T + +IATG RP PN E ++S G L +PK++ V+G GYI Sbjct: 126 ----NGETITADHILIATGGRPSH-PNIPGVEYGIDSDGFFELPALPKRVAVVGAGYIAV 180 Query: 190 ELGTAYANFGTELVILEGGDEILPGFEKQMSSLVTRRLKKKGNVEIHTNAMAKGVEERPD 249 EL G E + L F+ + + + +G ++HTNA+ + V + D Sbjct: 181 ELAGVINGLGAETHLFVRKHAPLRSFDPLIVETLVEVMNAEG-PQLHTNAIPQAVVKNAD 239 Query: 250 GVTVTFEVK-GEEKTVDADYVLITVGRRPNTDELGLEQVGIEMTDRGIVKTDKQCRTNVP 308 G ++T E++ G +TVD ++ +GR P TD L G++ D+G + DK TNVP Sbjct: 240 G-SLTLELEDGRSQTVDC--LIWAIGREPATDNFNLAATGVKTNDKGYIVVDKFQNTNVP 296 Query: 309 NIYAIGDIIEGPPLAHKASYEGKIAAEAIAGEPAE--IDYLGIPAVVFSEPELASVGYTE 366 IYA+GD L A G+ +E + + +DY IP VVFS P + +VG TE Sbjct: 297 GIYAVGDNTGAVELTPVAVAAGRRLSERLFNNKPDEHLDYSNIPTVVFSHPPIGTVGLTE 356 Query: 367 AQAKEEGLD--IVAAKFPFAANGRALSLNETDGFMKLITRKEDGLVIGAQIAGASASDMI 424 QA+E+ D + K F A A++ + MKL+ + ++G G +M+ Sbjct: 357 PQAREQYGDEAVKVYKSSFTAMYTAVTSHRQPCRMKLVCVGPEEKIVGIHGIGFGMDEML 416 Query: 425 SELSLAIEGGMTAEDIAMTIHAHPTLGE 452 ++A++ G T +D T+ HPT E Sbjct: 417 QGFAVALKMGATKKDFDNTVAIHPTAAE 444 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: 546 Number of extensions: 26 Number of successful extensions: 9 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: 450 Length adjustment: 33 Effective length of query: 437 Effective length of database: 417 Effective search space: 182229 Effective search space used: 182229 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 17 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