Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 5211244 Shew_3660 glutathione reductase (RefSeq)
Query= CharProtDB::CH_004665 (470 letters) >FitnessBrowser__PV4:5211244 Length = 451 Score = 211 bits (536), Expect = 5e-59 Identities = 143/454 (31%), Positives = 235/454 (51%), Gaps = 26/454 (5%) Query: 11 DTLVIGAGPGGYVAAIRAAQLGQKVTVVEKATLGGVCLNVGCIPSKALINAGHRYENAKH 70 D + +GAG GG +A RAA G KV ++E LGG C+NVGC+P K + G + A H Sbjct: 6 DYICLGAGSGGIASANRAAMRGAKVLLIEAKALGGTCVNVGCVPKKVMWY-GAQVAEAMH 64 Query: 71 --SDDMGITAENVTVDFTKVQEWKASVVNKLTGGVAGLLKGNKVDVVKGEAYFVDSNSVR 128 + D G D++K+ E + + + ++ G L N V +V+G FVD+N++ Sbjct: 65 LYAKDYGFDVSVNKFDWSKLVESREAYIERIHGAYDRGLDSNGVTLVRGYGQFVDNNTIE 124 Query: 129 VMDENSAQTYTFKNAIIATGSRPIELPNFKYSERVLNSTGALALKEIPKKLVVIGGGYIG 188 V E+ Y+ + +IATG P +PN +E ++S G AL E PK++ V+G GYI Sbjct: 125 VNGEH----YSADHILIATGGTPT-IPNIPGAEYGIDSDGFFALNEQPKRVAVVGAGYIA 179 Query: 189 TELGTAYANFGTELVILEGGDEILPGFEKQMSSLVTRRLKKKGNVEIHTNAMAKGVEERP 248 EL G+E + L F+ +S + + G +HT+++ + V + Sbjct: 180 VELAGVLHALGSETHLFVRKHAPLRSFDPMLSEALMESMATDGP-SLHTHSIPESVTKNA 238 Query: 249 DGVTVTFEVKGEEKTVDADYVLITVGRRPNTDELGLEQVGIEMTDRGIVKTDKQCRTNVP 308 DG ++T +++ E + + D ++ +GRRP+TD++GLE +++ D+G V D Q T Sbjct: 239 DG-SLTLKLENGE-SYEIDTLIWAIGRRPSTDKIGLENTDVKLNDKGYVVVDAQQNTTAK 296 Query: 309 NIYAIGDIIEG----PPLAHKASYEGKIAAEAIAG--EPAEIDYLGIPAVVFSEPELASV 362 IY +GDIIEG P+A KA G++ +E + A++DY +P VVFS P + ++ Sbjct: 297 GIYCVGDIIEGGIELTPVAVKA---GRLLSEHLFNGMTDAKMDYSLVPTVVFSHPAIGTM 353 Query: 363 GYTE----AQAKEEGLDIVAAKFPFAANGRALSLNETDGFMKLITRKEDGLVIGAQIAGA 418 G TE AQ EE + + + F + A++ + MKL+ ++ V+G G Sbjct: 354 GLTEPEAIAQYGEENVKVYNS--GFTSMYTAVTAHRQACKMKLVCAGKEEKVVGIHGIGY 411 Query: 419 SASDMISELSLAIEGGMTAEDIAMTIHAHPTLGE 452 +++ +AI+ G T D + HPT E Sbjct: 412 GMDEILQGFGVAIKMGATKADFDAVVAIHPTGAE 445 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: 528 Number of extensions: 27 Number of successful extensions: 6 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: 451 Length adjustment: 33 Effective length of query: 437 Effective length of database: 418 Effective search space: 182666 Effective search space used: 182666 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