Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; LPD; E3 component of pyruvate complex (uncharacterized)
to candidate 351070 BT1542 putative pyridine nucleotide-disulfide oxidoreductase (NCBI ptt file)
Query= curated2:P72740 (474 letters) >FitnessBrowser__Btheta:351070 Length = 457 Score = 186 bits (472), Expect = 1e-51 Identities = 147/472 (31%), Positives = 230/472 (48%), Gaps = 28/472 (5%) Query: 7 YDLVIIGAGVGGHGAALHAVKCGLKTAIIEAKD--MGGTCVNRGCIPSKALLAASGRVRE 64 YD +IIG G G A G + A++E D GG C N CIP+K L+ S E Sbjct: 4 YDAIIIGFGKAGKTLAAELSNRGWQVAVVEQSDEMYGGACPNVACIPTKTLIHES----E 59 Query: 65 MSDQDHLQQLGIQINGVTFTREAIAAHANDLVSKIQSDLTNSLT-RLKVDTIRGWGKVSG 123 +S + Q N R+AIA N L S ++ + L+ R V G G + Sbjct: 60 ISTLLYHNDFDKQSN---MYRQAIA-RKNKLTSFLRENNYEKLSKRPNVTIYTGKGSLVS 115 Query: 124 PQEVTVIGDNETRILKAKEIMLCPGSVPFVPP--GIEIDHKTVFTSDEAVKLETLPQWIA 181 V V E L+ KEI + GS P +P GI+ + V+TS ++L+ LP+ + Sbjct: 116 ANTVKVALPEEEIELQGKEIFINTGSTPIIPSIEGIQ-QSRNVYTSTTLLELDILPKHLI 174 Query: 182 IIGSGYIGLEFSDVYTALGCEVTMIEALPDLMPGFDPEIAKIAERVLIKSRDIETYTGVF 241 I+G GYIGLEF+ +Y G +VT++EA MP D +IAK V+ K + +E V Sbjct: 175 IVGGGYIGLEFASMYAGFGSKVTLLEAGNRFMPRNDSDIAKSVREVMEK-KGVEIRLNVR 233 Query: 242 ATKIKAGSPVEIELTDAKTKEVID-TLEVDACLVATGRIPATKNLGLETVGVETDRRGFI 300 I + + LT + T + ++ DA L+ATGR P + L L+ GVE D G I Sbjct: 234 TQSIH-DTHDGVTLTYSDTSDGTPYFVDGDAILIATGRKPMIEGLNLQAAGVEVDAHGAI 292 Query: 301 EVNDQMQVIKDGKPVPHLWAVGDATGKMMLAHAASGQGVVAVENICG-RKTEVDYR-AIP 358 VNDQ+ PH+WA+GD G + + + + + G +K +++ R +P Sbjct: 293 VVNDQLHT-----NAPHIWAMGDVKGGAQFTYVSLDDFRIIRDQLFGDKKRDINDRDPLP 347 Query: 359 AAAFTHPEISYVGLTEAQAKELGEKEGFVVSTAKTYFKGNSKALAEKETDGIAKVVYRQD 418 A F P ++++G+TE +A G F VS S+ L ++TDG+ K + Sbjct: 348 YAVFIDPPLAHIGITEEEALRKG--YSFKVSRLPATSVVRSRTL--QQTDGMLKAIINSH 403 Query: 419 TGELLGAHIIGIHASDLIQEAAQAIADRKSVRELAFHVHAHPTLSEVLDEAY 470 +G+++G + A +LI A A+ ++ L + HP++SE L++ + Sbjct: 404 SGKIMGCTMFCTDAPELINMVAMAMKTGQTSTFLRDFIFTHPSMSEGLNQLF 455 Lambda K H 0.317 0.134 0.384 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: 453 Number of extensions: 18 Number of successful extensions: 8 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: 474 Length of database: 457 Length adjustment: 33 Effective length of query: 441 Effective length of database: 424 Effective search space: 186984 Effective search space used: 186984 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