Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex (uncharacterized)
to candidate WP_046007564.1 OLEAN_RS00325 pyridine nucleotide-disulfide oxidoreductase
Query= curated2:O84561 (465 letters) >NCBI__GCF_000967895.1:WP_046007564.1 Length = 717 Score = 237 bits (605), Expect = 8e-67 Identities = 144/451 (31%), Positives = 239/451 (52%), Gaps = 22/451 (4%) Query: 8 VVIGAGPGGYVAAITAAQAGLKTALIEKREAGGTCLNRGCIPSKALLAGAEVVTQIRHAD 67 +VIG G G V++I + K LIEK + GG CLN GC+PSKA++ A++V + + + Sbjct: 245 IVIGGGAAGLVSSIIGSAVKAKVTLIEKHKMGGDCLNTGCVPSKAIIHAAKIVHENKKS- 303 Query: 68 QFGIHVEGFSINYPAMVQRKDSVVRSIRDGLNGLIRSNKITVFSGRG--------SLISS 119 H G + PA V + V+ + D + + + + + G G +IS Sbjct: 304 ----HSTGLLLGEPASVDFQ-KVMTHVHDSIKAIEPHDSVERYEGLGVSCATGQAKIISP 358 Query: 120 TEVKILGENPSVI--KAHSIILATGSEPRAFPGIPFSAESPRILCSTGVLNLKEIPQKMA 177 EV+I + +V A +II+ATG PR P IP + S + + +P+++ Sbjct: 359 WEVEIQHASGAVEIRSAANIIIATGGRPR-IPKIP-GLDQVTYYTSDTLWQITALPKRLL 416 Query: 178 IIGGGVIGCEFASLFHTLGSEVSVIEASSQILALNNPDISKTMFDKFTRQGLRFVLEASV 237 I+G G IGCE F LGS+V++++ ++ + D+S+ + D +G+ V S+ Sbjct: 417 ILGAGPIGCELGQAFARLGSQVTMVDKGQFLMPREDEDVSQLVADAMVAEGVNHVPGRSI 476 Query: 238 SNIEDIGDRVRLTI-NGNVEEYDYVLVSIGRRLNTENIGLDKAGVICDERGVIPTDATMR 296 S E + NG+ E+D +L++IGR NTE++GL+ ++ D G + D ++ Sbjct: 477 SKFEPSNSGHSAVLDNGDAIEFDALLLAIGREGNTEHLGLENVDLVTDNNGFLAVDEYLQ 536 Query: 297 TNVPNIYAIGDITGKWQLAHVASHQGIIAARN-IAGH--KEEIDYSAVPSVIFTFPEVAS 353 T P IYA GD+ G +Q HV++H+ AA N + G + + DY +P FT PEVA Sbjct: 537 TECPTIYACGDVIGGYQFTHVSAHEAWFAAVNSLFGRFKRFKADYRVIPWATFTSPEVAR 596 Query: 354 VGLSPTAAQQQKIPVKVTKFPFRAIGKAVAMGEADGFAAIISHETTQQILGAYVIGPHAS 413 VG+S A++Q IP + T++ + +A+ A GF +++ +ILGA ++GP A Sbjct: 597 VGISEKEAKRQNIPYESTQYGLDDLDRAITDDAATGFVRVLTVPGKDKILGATIVGPRAD 656 Query: 414 SLISEITLAVRNELTLPCIYETIHAHPTLAE 444 LI+ + +++ L L + TIHA+PT E Sbjct: 657 DLIATFVIGMKHGLGLNKVLGTIHAYPTYME 687 Lambda K H 0.319 0.135 0.388 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: 753 Number of extensions: 33 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: 1 Length of query: 465 Length of database: 717 Length adjustment: 36 Effective length of query: 429 Effective length of database: 681 Effective search space: 292149 Effective search space used: 292149 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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