Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex (uncharacterized)
to candidate H281DRAFT_00438 H281DRAFT_00438 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component
Query= curated2:O84561 (465 letters) >FitnessBrowser__Burk376:H281DRAFT_00438 Length = 466 Score = 239 bits (609), Expect = 2e-67 Identities = 146/456 (32%), Positives = 230/456 (50%), Gaps = 13/456 (2%) Query: 1 MNEAFDCVVIGAGPGGYVAAITAAQAGLKTALIEKREAGGTCLNRGCIPSKALLAGAEVV 60 M + FD VVIG G GG A+ ++G +TA+IE+ GGTC+N GC P+KA +A A Sbjct: 1 MAQHFDAVVIGTGQGGAPLAVRLGKSGRRTAVIERAAFGGTCVNVGCTPTKAYVASARAA 60 Query: 61 TQIRHADQFGIHVEG-FSINYPAMVQRKDSVVRSIRDGLNGLIR-SNKITVFSGRGSLIS 118 RHA + G+H+ G ++ A+ RKD +V DG+ +R + +TVF+G Sbjct: 61 HVARHAARLGVHIGGAVGVDMAAVKARKDKIVGQSHDGVEAWLRGARNLTVFTGHARFTG 120 Query: 119 STEVKILGENPSV---IKAHSIILATGSEPRAFPGIPFSAESPRILCSTGVLNLKEIPQK 175 + + G + +V + A I L TG+ RA E R ++ +L + E+P + Sbjct: 121 PHTLAVSGPDGAVLHELSADEIFLNTGT--RAVVPPLEGIERARYYTNSSLLEITELPSR 178 Query: 176 MAIIGGGVIGCEFASLFHTLGSEVSVIEASSQILALNNPDISKTMFDKFTRQGLRFVLEA 235 + I+GG I EFA +F GSEV+V+ ++L + D ++++ R+G+ F Sbjct: 179 LVIVGGSYIALEFAQVFRRFGSEVTVLVRGDRVLTREDADFAESVQSVLAREGVEFRFGV 238 Query: 236 SVSNIEDIGDR---VRLTINGNVE--EYDYVLVSIGRRLNTENIGLDKAGVICDERGVIP 290 S +E R V + NV E ++L + GR+ NT+++GL AG+ D G IP Sbjct: 239 QPSRVEPHPHRENEVCIGFEQNVPALEASHLLFATGRKPNTDDLGLAAAGIETDRHGTIP 298 Query: 291 TDATMRTNVPNIYAIGDITGKWQLAHVA-SHQGIIAARNIAGHKEEIDYSAVPSVIFTFP 349 D +RTNVP ++AIGDI G+ H + I+AA G +D + +F P Sbjct: 299 VDGQLRTNVPGVWAIGDINGRGAFTHTSYDDYQIVAANLFDGGTRTVDKRIMAYAVFVDP 358 Query: 350 EVASVGLSPTAAQQQKIPVKVTKFPFRAIGKAVAMGEADGFAAIISHETTQQILGAYVIG 409 +A VGLS ++ + P +G+A GE DGF +++ T+QILGA + G Sbjct: 359 PLARVGLSEDDVRKSGRDALIATMPMSRVGRARERGETDGFMKVLADPHTRQILGAAIHG 418 Query: 410 PHASSLISEITLAVRNELTLPCIYETIHAHPTLAEV 445 I I + P + +H HPT++E+ Sbjct: 419 IEGDEAIHTIIDIMTAGAPYPTLQYAMHIHPTISEL 454 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: 508 Number of extensions: 21 Number of successful extensions: 5 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: 466 Length adjustment: 33 Effective length of query: 432 Effective length of database: 433 Effective search space: 187056 Effective search space used: 187056 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: 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