Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 203771 SO4702 glutathione reductase (NCBI ptt file)
Query= SwissProt::P85207 (461 letters) >FitnessBrowser__MR1:203771 Length = 451 Score = 201 bits (512), Expect = 3e-56 Identities = 152/452 (33%), Positives = 228/452 (50%), Gaps = 24/452 (5%) Query: 4 YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKAL---LHAAETVH 60 +D I +G G GG +A R A G KVL +EA VGG C+NVGC+P K + H AE ++ Sbjct: 5 FDYICLGAGSGGIASANRAAMRGAKVLLIEAKHVGGTCVNVGCVPKKVMWYGAHIAEAMN 64 Query: 61 HLKGAEGFGLKAKPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGPREI 120 GF + + D L R+ + ++ NKV LL G+ RF I Sbjct: 65 LYAKDYGFDVSVN-KFDWNTLVNSREAYIGRIHEAYGRGFTNNKVTLLNGYGRFVNGNTI 123 Query: 121 EVNGETYGAQSFIIATGSEPM--PLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGAVG 178 EVNGE Y A +IATG P + G +G D D ALR + PKR+ V+G G + Sbjct: 124 EVNGEHYTADHILIATGGAPTIPNIPGAEYGIDS-DGFFALREQ---PKRVAVVGAGYIA 179 Query: 179 LELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKK-Q 237 +E+ + H LGSE L L D L A++ EG + T + K Sbjct: 180 VEVAGVLHALGSETHLFVRKHAPLRNFDPMLIDALVDAMKTEGPTLHTNSVPQSVVKNAD 239 Query: 238 DGLHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETS 297 D L + LE + E + VD ++ A+GR P T +GLE V++D +G++ +A+ T+ Sbjct: 240 DSLTLNLE-----NGESVTVDCLIWAIGRSPATGNIGLENTEVQLDSKGYVITDAQQNTT 294 Query: 298 APGVYAIGDV-ARPPLLAHKAMKEGLVAAENA--AGKNALFDF-QVPSVVYTGPEWAGVG 353 G+Y +GD+ A L A+K G + +E A +A D+ Q+P+VV++ P +G Sbjct: 295 HKGIYCVGDIMAGGVELTPVAVKAGRLLSERLFNAMSDAKMDYSQIPTVVFSHPPIGTMG 354 Query: 354 LTEEEARKAGY---NVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQA 410 LTE EAR A Y NVKV F++ A+T +K+V + D ++G+ +G Sbjct: 355 LTEPEAR-AQYGDGNVKVYTSSFTSMYTAVTSHRQACKMKLVCAGKEDKVVGIHGIGFGM 413 Query: 411 GELIAEATLALEMGATVSDLGLTIHPHPTLSE 442 E++ +A++MGAT +D + HPT +E Sbjct: 414 DEILQGFGVAMKMGATKADFDAVVAIHPTGAE 445 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: 548 Number of extensions: 37 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: 461 Length of database: 451 Length adjustment: 33 Effective length of query: 428 Effective length of database: 418 Effective search space: 178904 Effective search space used: 178904 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 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