Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate WP_028309849.1 H566_RS0100245 glutathione-disulfide reductase
Query= SwissProt::P11959 (470 letters) >NCBI__GCF_000482785.1:WP_028309849.1 Length = 452 Score = 207 bits (526), Expect = 8e-58 Identities = 133/443 (30%), Positives = 214/443 (48%), Gaps = 10/443 (2%) Query: 11 ETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQAKH 70 + +GAG GG + AA G +V I E +GG C+ GC+P K + AS + Sbjct: 7 DLFTLGAGSGGVSGSRYAASKGARVAICEDSRVGGTCVIRGCVPKKLFMYASQFSDAFGD 66 Query: 71 SEEMGIKAENVTIDFAKVQEWKASVVKKLTGGVEGLLKGNKVEIVKGEAYFVDANTVRVV 130 + G + D A +Q K+ +L G +L + V +V+G +DA+TV V Sbjct: 67 AAGYGWTVPEASFDMATLQAAKSKETARLEGIYRTMLGNSGVALVEGRGRVIDAHTVEV- 125 Query: 131 NGDSAQTYTFKNAIIATGSRPIELPNFKFSNRILDSTGALNLGEVPKSLVVIGGGYIGIE 190 + + YT + ++ATG +P P + S L+L E P L+V+G GYI +E Sbjct: 126 ---AGKAYTAERILVATGGKPAA-PAIPGIELAMTSNEILDLAERPARLLVLGAGYIAVE 181 Query: 191 LGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAEEREDGV 250 + FG+ VT+ L GF++ + + + +G+ + A + E+ G Sbjct: 182 FAGIFRGFGSAVTVAFRGDAPLRGFDEDLRRRLATEMTNRGITLAAG-FAPASIEKAGGE 240 Query: 251 TVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNR-GLIEVDQQCRTSVPNI 309 + A+G + AD VL +GR PN+ LGLE+ G+++ + G + VD RTSVP I Sbjct: 241 FIVRGADGSE--LRADAVLNALGRVPNSAGLGLEEAGVRIDAKTGAVVVDAFSRTSVPGI 298 Query: 310 FAIGDIVPGPALAHKASYEGKVAAEA-IAGHPSAVDYVAIPAVVFSDPECASVGYFEQQA 368 FA+GD+ AL A E + + G +D+ + + VFS P S+G EQ A Sbjct: 299 FAVGDVTNRIALTPVAIAEARAFVDTEFGGAARHIDHALVASAVFSQPPIGSIGLSEQAA 358 Query: 369 KDEGIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDMIAELGL 428 K +G DV + F ++ + ++KLVV + ++G +IG +A +++ + Sbjct: 359 KAKGFDVTVFESDFRPMKNTISGRNERSYMKLVVDRASDKVLGLHMIGVDAGELVQGFAV 418 Query: 429 AIEAGMTAEDIALTIHAHPTLGE 451 A+ G T D TI HPT GE Sbjct: 419 AVTMGATKADFDRTIAVHPTAGE 441 Lambda K H 0.316 0.135 0.376 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: 480 Number of extensions: 36 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: 452 Length adjustment: 33 Effective length of query: 437 Effective length of database: 419 Effective search space: 183103 Effective search space used: 183103 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