Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes (uncharacterized)
to candidate 8499450 DvMF_0222 FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)
Query= curated2:Q8KCW2 (469 letters) >FitnessBrowser__Miya:8499450 Length = 473 Score = 279 bits (714), Expect = 1e-79 Identities = 181/481 (37%), Positives = 259/481 (53%), Gaps = 28/481 (5%) Query: 6 TLAAQFDVAVIGSGPGGYEAAIHAARYGLKTCIVEKAVLGGVCVNWGCIPTKALLRSAEV 65 T + ++D+ ++G GPGG AA AA GL +V++ LGG C+N GCIPTK LL + Sbjct: 2 TPSTRYDMIILGGGPGGSRAAFDAAARGLSVALVDRDGLGGTCLNRGCIPTKLLLGATAA 61 Query: 66 FDLAKNPETFGVNVGNVSFDLAQAVKRSRNVALKSSKGVAYLLKKAAVEVLAGEAVLTGG 125 L + + G+++FDL +R + + + LK A + V AGE +TG Sbjct: 62 LPLLETQKKLKGADGHIAFDLPALQQRKDRYVKGTRQALEKRLKAAGIAVYAGEGRVTGE 121 Query: 126 A--------GVMVTMPDGSVR--MLGAKNIIVATGSTPRVIPGLEPDGKKIITSREALIL 175 V+ DG+ + LG +IVATGSTP PGL DG ++ S L + Sbjct: 122 RQGDADGELAVVAAQADGTTQETRLGWGTLIVATGSTPASFPGLAADGAAVLDSTALLDV 181 Query: 176 KEVPKSMIVVGGGAIGVEMAWFYAKAGSKVTIVELMPRMLPAEEAEVSEALKRSFEKAGI 235 E P+S+IVVGGGAIG+EMA F+++ G+++TIVE M R+ P E+AEV + L++ + + G Sbjct: 182 TEAPESLIVVGGGAIGLEMADFFSRFGTRITIVEGMGRLAPTEDAEVGDTLRKVYAREGW 241 Query: 236 TVHCGAKLDNVAVSESGVSAELVVEGSAPQTLNASCLLVAVGVTGAIDGLGLDAVGVETE 295 T+H G K+ ++A V V+ + L AS L+AVG A G+GL+A+G Sbjct: 242 TIHNGRKVASLAT----VDGHAVLRFEDGEELTASKALLAVGRRPASVGIGLEALGTTLR 297 Query: 296 -RGFIRTDGQCRTSAPGIYAIGDVRGGMLLAHKASAEAAIAVEAIAGKSPEPLSEPLIPR 354 G+++TD R +AP +YAIGDV G LLAH A +A AV G + P ++P Sbjct: 298 GPGWMQTDEWLR-AAPHVYAIGDVNGRTLLAHAADHQARYAVRHACGDTAAPYDAGVMPA 356 Query: 355 CVYAQPSVASVGLTEEAAVNAGYQVAVGRSQFAASGKANAYGQLEGFVKLVFDAATGKML 414 C+Y VG T E NAG+ V RS A+ A AYG +GF+K+V+ G++ Sbjct: 357 CIYGHLEAMRVGPTAEELKNAGFSPRVSRSMLIANPIAQAYGTTQGFIKIVW--VDGRIR 414 Query: 415 GGHLIGHD-------AVELIGELGLACRYGVTAGGLVNTVHAHPTLSETVREAAFDALQS 467 G +GH A L G G A G TA N + AHPTL E + EAA +A Q Sbjct: 415 GVTAVGHGVSHLVTLAAVLAGGSGTAT--GWTAHDAGNVIFAHPTLDEAL-EAAIEAPQE 471 Query: 468 M 468 + Sbjct: 472 L 472 Score = 24.6 bits (52), Expect = 0.007 Identities = 13/36 (36%), Positives = 18/36 (50%) Query: 5 DTLAAQFDVAVIGSGPGGYEAAIHAARYGLKTCIVE 40 D A + V+G G G E A +R+G + IVE Sbjct: 180 DVTEAPESLIVVGGGAIGLEMADFFSRFGTRITIVE 215 Lambda K H 0.316 0.133 0.377 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: 635 Number of extensions: 31 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 469 Length of database: 473 Length adjustment: 33 Effective length of query: 436 Effective length of database: 440 Effective search space: 191840 Effective search space used: 191840 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