Align TPP-dependent acetoin dehydrogenase complex, E3 component, dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_011913245.1 PST_RS10695 glutathione-disulfide reductase
Query= CharProtDB::CH_006552 (578 letters) >NCBI__GCF_000013785.1:WP_011913245.1 Length = 452 Score = 236 bits (601), Expect = 2e-66 Identities = 145/448 (32%), Positives = 243/448 (54%), Gaps = 17/448 (3%) Query: 117 NLVVIGGGPGGYVAAIRAAQLGAKVTLIEKESLGGTCLNVGCIPTKVLLHSSQLLTEMKE 176 +L VIG G GG AA AA GAKV + E LGGTC+NVGC+P K+L++ + ++ + Sbjct: 6 DLFVIGAGSGGVRAARFAAGFGAKVAVAESRYLGGTCVNVGCVPKKLLVYGAHYAEDIGQ 65 Query: 177 GDKLGIDIEGSIVVNWKHIQKRKKIVIKKLVSGVSGLLTCNKVKVIKGTAKFESKDTILV 236 G I+G+ +WK + K I++L +L + V +++ A+ T+ V Sbjct: 66 AQGYGWTIDGA-TFDWKTLIANKDREIQRLNGIYRSILVDSGVTLLQAHAQLVDAHTVEV 124 Query: 237 TKEDGVAEKVNFDNAIIATGSMPFIPEIEGNKLSGVIDSTGALSLESNPESIAIIGGGVI 296 ++ + ++ +IATG P +PEI G + I S A L++ P + ++GGG I Sbjct: 125 E-----GKRYSAEHILIATGGWPHVPEIPGRE--HAITSNEAFYLDALPRRVLVVGGGYI 177 Query: 297 GVEFASIFNSLGCKVSIIEMLPHILPPMDREISEIAKAKLIRDGININNNCKVTRIEQGE 356 VEFASIF+ G ++ L D + + K ++I+ G+++ N + I++ Sbjct: 178 AVEFASIFHGCGADTKLLYRGELFLRGFDGSLRDHLKDEMIKKGVDLQFNADIVHIDKLA 237 Query: 357 DGLKVSFIGDKGEESIDVEKVLIAVGRRSNIEGLDVEKIGVKTEG-GSIIVNDKMETNVE 415 DG ++ + D +++ + + A GRR I+G+ +E GV + G + V+D+ T+V Sbjct: 238 DGSLLATLED--GRTLEADCIFYATGRRPMIDGVGLEAAGVALDARGFVAVDDEYRTSVP 295 Query: 416 GIYAIGDCTGKIMLAHVASDQGVVAAENIM--GQNKKMDYKTVPACVYTKPELASVGLTE 473 I AIGD G++ L VA +G+ A + Q +K+DY T+P V++ P +A+VGLTE Sbjct: 296 SILAIGDVIGRVQLTPVALAEGMAVARRLFKPEQYRKVDYSTIPTAVFSLPNMATVGLTE 355 Query: 474 EQAKEKGIDYKVGKFQLAANGKSLIMNET--GGVIKIITDKKYEEILGVHILGPRATDLI 531 EQA+E+G YKV F+ L M ++ ++K++ D + +LG H+ GP A +++ Sbjct: 356 EQAREQG--YKVTLFESRFRPMKLTMTDSLERSLMKLVVDAHTDRVLGCHMAGPDAGEIM 413 Query: 532 TEAALALRLEATLEEIITTVHAHPTVGE 559 A+AL+ AT + T+ HPT E Sbjct: 414 QGLAVALKAGATKQVFDETLGIHPTAAE 441 Lambda K H 0.313 0.134 0.365 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: 529 Number of extensions: 22 Number of successful extensions: 7 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: 578 Length of database: 452 Length adjustment: 35 Effective length of query: 543 Effective length of database: 417 Effective search space: 226431 Effective search space used: 226431 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: 52 (24.6 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