Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes (uncharacterized)
to candidate WP_002880338.1 B506_RS08325 NAD(P)/FAD-dependent oxidoreductase
Query= curated2:P95596 (454 letters) >NCBI__GCF_000387565.1:WP_002880338.1 Length = 443 Score = 140 bits (353), Expect = 8e-38 Identities = 129/427 (30%), Positives = 195/427 (45%), Gaps = 36/427 (8%) Query: 1 MAEFDVIIIGGGPGGYVCAIRCAQLGLKTACVEGRGALGGTCLNVGCIPSKALLHATHEL 60 M ++D IIIG GP + A+ +TA V GGTC N GC P L A + Sbjct: 1 MKKYDYIIIGSGPAANHLLFKLARTD-RTALVIENNLWGGTCPNTGCQPKIFLEGAVRPV 59 Query: 61 HEVHENFEKMGLMGAKVKVDWAKIDGNTKGIEFLFK--------KNKVTYLRGWGSIPAP 112 + K + A ++DW + K I F+ ++V + G G I P Sbjct: 60 LNTYYLTGKG--VKAAAQLDWKTLIKRKKEIWAKFRAEERSSIESDQVDTVFGSGVITGP 117 Query: 113 GQVKVGDEVHTAKNIVIATGSESSGL--PGIEIDEQTVVTSTGALSLAKVPKSMVVIGAG 170 V E + NI+IATG L PG E +++ L ++PK VVIG G Sbjct: 118 HTVAAAGEEYEGINIIIATGLLPHHLEVPGSEY----AISNDEFFDLDELPKKAVVIGGG 173 Query: 171 VIGLELGSVYARLGAEVTVVEYLDAITPGMDAEVAKGLQRILTRQGLKFVLGAAVQGVDK 230 + LEL ++ G+EVTV+++ + + D E + L I+ +G+ L V K Sbjct: 174 YVALELSTILQAAGSEVTVLQHSEKLLRAFDQEYVEKLTEIMEERGIVIHLNTPV----K 229 Query: 231 AKGKNTVRYTLRKDESAHAIEAEVVLVATGRKPFTKGLGLEALGVEMLPRGQVKADSHWA 290 A KN+ Y + E+ E ++V+ A+GR+ GLGLE LG++ P V + H Sbjct: 230 AIAKNSAAYEVTA-ENGQKFETDLVIDASGRRANVNGLGLEKLGIKFDPVKGVAVNEHLQ 288 Query: 291 TNVPGLYAIGD-AIVGPM-LAHKAEDEGMAVAEVIA-GKHGHVNYDVIPGVIYTTPEVAA 347 TNVP ++A GD A G M L A + + + + G + Y + +T P+VA Sbjct: 289 TNVPSIFAAGDVADNGQMNLTPVAWVDSYHIYDFVENGLTEGIKYPAVATSTFTYPQVAQ 348 Query: 348 VGKTEDALKQEG--RAYKVGK-FSFMGNG----RAKAVFQAEGFV----KILADAATDRI 396 VGK E + + R K+G F+ +G G K +F +G V +I +A D Sbjct: 349 VGKRESEMAEGDTVRRMKLGSTFAALGEGDEEAELKVIFNKDGEVVGASEISINAGEDIN 408 Query: 397 LGAHIIG 403 L A +IG Sbjct: 409 LFAPLIG 415 Lambda K H 0.318 0.136 0.397 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: 467 Number of extensions: 33 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: 454 Length of database: 443 Length adjustment: 33 Effective length of query: 421 Effective length of database: 410 Effective search space: 172610 Effective search space used: 172610 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 (21.7 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