Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex (uncharacterized)
to candidate GFF3909 HP15_3849 pyridine nucleotide-disulfide oxidoreductase dimerization region
Query= curated2:O84561 (465 letters) >FitnessBrowser__Marino:GFF3909 Length = 729 Score = 253 bits (646), Expect = 2e-71 Identities = 160/467 (34%), Positives = 253/467 (54%), Gaps = 32/467 (6%) Query: 5 FDCVVIGAGPGGYVAAITAAQAGLKTALIEKREAGGTCLNRGCIPSKALLAGAEVVTQIR 64 ++ +VIG G G V+A AA K ALIEK + GG CLN GC+PSKAL+ A+ +R Sbjct: 238 YNLLVIGGGSAGLVSAYIAAAVKAKVALIEKHKMGGDCLNTGCVPSKALIRSAKAADTLR 297 Query: 65 HADQFGIHVEGFSINYPAMVQRKDSVVRSIRDGLNGLIRSNKITV--FSGRGSLISSTEV 122 HA+++G+ ++ ++ R +V+ + + R K+ V +G S +S E+ Sbjct: 298 HANRYGLESVPVKGSFKNIMNRVKNVIAKVEPH-DSPERYRKLGVDCIAGEASFVSPWEL 356 Query: 123 KILGENPSV--IKAHSIILATGSEPRAFPGIPFSAESPRILCSTGVLNLKEIPQKMAIIG 180 ++ + + A SI++ATG +P A P IP + L S + L+E P+++ ++G Sbjct: 357 EVRHNDGRTERLTARSIVVATGGKP-AVPPIP-GLKDMEPLTSDNLWELQEQPERLLVLG 414 Query: 181 GGVIGCEFASLFHTLGSEVSVIEASSQILALNNPDISKTMFDKFTRQGLRFVLEAS---- 236 GG IG E A F LGS+V+ +E ++LA + D+S+ + +F G+ L+ + Sbjct: 415 GGPIGSELAHAFARLGSKVTQVEMGERLLAKEDEDVSELVLKQFQADGVDVRLKHAAAEF 474 Query: 237 -------VSNIEDIGDRVRLTINGNVEEYDYVLVSIGRRLNTENIGLDKAGVICDERGVI 289 V+ E G+RVR+ +D VLV++GR NT + L++ GV G + Sbjct: 475 RMEEGEKVAYCEHEGERVRIP-------FDQVLVAVGRAANTAGLNLERIGVDTLPNGTV 527 Query: 290 PTDATMRTNVPNIYAIGDITGKWQLAHVASHQGIIAARN-IAGH--KEEIDYSAVPSVIF 346 P + M PN++A GD+ G +Q H A+HQ AA N + G + ++DY +P V F Sbjct: 528 PVEEDMSLRYPNVFACGDVAGPYQFTHAAAHQAWYAAVNGLFGQFKRFKVDYRVMPWVTF 587 Query: 347 TFPEVASVGLSPTAAQQQKIPVKVTKFPFRAIGKAVAMGEADGFAAIISHETTQQILGAY 406 T PEVA VGLS A Q + +VT++ + +A+A E GF +++ +ILGA Sbjct: 588 TSPEVARVGLSEAEATAQGVAYEVTRYGLDDLDRAIAESEDHGFIKVLTPPGKDKILGAV 647 Query: 407 VIGPHASSLISEITLAVRNELTLPCIYETIHAHPTLAEVWAESALLA 453 V+G HA +++E TLA+++ L L I TIH +PT W ESA A Sbjct: 648 VVGSHAGEILAEFTLAMKHGLGLNKILGTIHPYPT----WNESAKYA 690 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: 710 Number of extensions: 31 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: 465 Length of database: 729 Length adjustment: 36 Effective length of query: 429 Effective length of database: 693 Effective search space: 297297 Effective search space used: 297297 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 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