Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 (characterized)
to candidate 3606907 Dshi_0335 pyridine nucleotide-disulphide oxidoreductase dimerisation region (RefSeq)
Query= SwissProt::P11959 (470 letters) >FitnessBrowser__Dino:3606907 Length = 470 Score = 220 bits (560), Expect = 9e-62 Identities = 154/455 (33%), Positives = 238/455 (52%), Gaps = 18/455 (3%) Query: 8 IETETLVVGAGPGGYVAAIRAAQLGQKVTIVEKGNLGGVCLNVGCIPSKALISASHRYEQ 67 IET+ V+GAG GG A A Q+G +V ++E +GG CLN GC+PSKALI+A + Sbjct: 5 IETDICVIGAGSGGLSVAAGAVQMGARVVLIEGHLMGGDCLNFGCVPSKALIAAG-KQAH 63 Query: 68 AKHSEEMGIKAENVTIDFAKVQEWKASVVKKLTG-GVEGLLKGNKVEIVKGEAYFVDANT 126 + G+ ID+A ++ V+ + + +G +++ A F+ Sbjct: 64 IVRAGGFGVAPAEPVIDYAAAKDHVRRVIDTIAPVDSQERFEGLGCTVIREYASFISETE 123 Query: 127 VRVVNGDSAQTYTFKNAIIATGSRPI--ELPNFKFSNRILDSTGALNLGEVPKSLVVIGG 184 ++ GD+ T + +IATGSRP +P + + T +L E P+ L++IGG Sbjct: 124 LQA--GDT--VITARRFVIATGSRPFVPPIPGVEDVPYYTNET-IFDLREKPEHLIIIGG 178 Query: 185 GYIGIELGTAYANFGTKVTILEGAGEILSGFEKQMAAIIKKRLKKKGVEVVTNALAKGAE 244 G IG+E+ A+ G KVT+LEGA + L + ++AAI +RL+ +G+E++ A A Sbjct: 179 GPIGMEMAQAHVRLGCKVTVLEGA-QALGKDDPELAAIALERLRGEGIEIIEGAQASNIS 237 Query: 245 EREDGVTVTYEANGETKTIDADYVLVTVGRRPNTDELGLEQIGIKMTNRGLIEVDQQCRT 304 + +TV ANG++ T ++L+ VGR PN D+L LE G+ RGL +VD RT Sbjct: 238 GKGGAITVE-TANGQSVT--GTHLLMAVGRTPNLDKLNLEAAGVDYDRRGL-KVDASLRT 293 Query: 305 SVPNIFAIGDIVPGPALAHKASYE-GKVAAEAIAGHPSAVDYVAIPAVVFSDPECASVGY 363 + I+ GD+ H A Y G + + + G P+ +P ++DPE A VG Sbjct: 294 TNKRIYGAGDVAGPLQFTHVAGYHAGILIRQLVLGLPAKTRDDHVPWATYTDPEIAQVGL 353 Query: 364 FEQQAKDE-GIDVIAAKFPFAANGRALALNDTDGFLKLVVRKEDGVIIGAQIIGPNASDM 422 E QA+++ G + A+F + N RA+A T G +K++V K G IGA I+G A ++ Sbjct: 354 TEAQAREKYGAALEVARFEYDENDRAIASGKTTGLIKVMVVK--GRPIGASIVGAEAGEL 411 Query: 423 IAELGLAIEAGMTAEDIALTIHAHPTLGEIAMEAA 457 I AI +A I +PTLGEI AA Sbjct: 412 IGLWAYAIANKHKMSAVANMIAPYPTLGEINKRAA 446 Lambda K H 0.316 0.135 0.376 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: 545 Number of extensions: 35 Number of successful extensions: 11 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: 470 Length of database: 470 Length adjustment: 33 Effective length of query: 437 Effective length of database: 437 Effective search space: 190969 Effective search space used: 190969 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