Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_090438938.1 BLS63_RS01735 glutathione-disulfide reductase
Query= SwissProt::P85207 (461 letters) >NCBI__GCF_900100495.1:WP_090438938.1 Length = 452 Score = 251 bits (642), Expect = 3e-71 Identities = 164/443 (37%), Positives = 234/443 (52%), Gaps = 10/443 (2%) Query: 4 YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63 +DL VIG G GG AA A G +V E+ +GG C+NVGC+P K L++ A + Sbjct: 5 FDLFVIGAGSGGVRAARFAAGYGARVAVAESRYLGGTCVNVGCVPKKLLVYGAHFAEDFE 64 Query: 64 GAEGFGLK-AKPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGPREIEV 122 A+GFG D L A ++ + +L G LL G+ V LL G AR +E Sbjct: 65 QAQGFGWSLGDARFDWPTLIANKNREIARLNGIYRNLLLGSGVTLLEGHARLLDEHRVEF 124 Query: 123 NGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGAVGLELG 182 G+ Y A+ ++ATG P + P E S A +E+ +PKR+LV+GGG + +E Sbjct: 125 GGQRYSARHILLATGGWPH-IPDIPGHEHAIGSNEAFFLEQ-LPKRVLVVGGGYIAVEFA 182 Query: 183 QIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQDGLHV 242 I+H LG+E +L+ L D LR L K GL ++ +K+ DG Sbjct: 183 SIFHGLGAETSLLYRRELFLRGFDGAVRTHLRDELSKRGLDLQFNCDIERIDKQADGS-- 240 Query: 243 LLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAPGVY 302 LL Q G + + D + A GRRP + LGLE GV++DERGFI+V+ + +TSAP + Sbjct: 241 LLAILQDGRR--LATDCVFYATGRRPMLDNLGLENTGVELDERGFIKVDEQFQTSAPSIL 298 Query: 303 AIGDVARPPLLAHKAMKEGLVAAENAAGKNAL--FDFQ-VPSVVYTGPEWAGVGLTEEEA 359 AIGDV L A+ EG+ A D+Q +P+ V++ P VGL+EE+A Sbjct: 299 AIGDVIGRVQLTPVALAEGMAVARRLFKPEEYRPVDYQSIPTAVFSLPNIGTVGLSEEQA 358 Query: 360 RKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEATL 419 + AG+ VKV + F LT L+K+V DA++D +LG +VGP+AGE+I + Sbjct: 359 KAAGHQVKVYESRFRPMKLTLTDCQERTLMKLVVDADSDRVLGCHMVGPEAGEIIQGLAV 418 Query: 420 ALEMGATVSDLGLTIHPHPTLSE 442 AL+ GAT TI HPT +E Sbjct: 419 ALKAGATKRIFDETIGVHPTAAE 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: 528 Number of extensions: 31 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: 452 Length adjustment: 33 Effective length of query: 428 Effective length of database: 419 Effective search space: 179332 Effective search space used: 179332 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