Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate 8500135 DvMF_0898 pyridine nucleotide-disulphide oxidoreductase dimerisation region (RefSeq)
Query= SwissProt::P85207 (461 letters) >FitnessBrowser__Miya:8500135 Length = 508 Score = 217 bits (552), Expect = 8e-61 Identities = 169/484 (34%), Positives = 231/484 (47%), Gaps = 50/484 (10%) Query: 5 DLIVIGTGPGGYPAAIRGAQLGLKV-LAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63 DL+VIG G G AA A+ G +V LA +GG CL+ GC+P+K LL A H ++ Sbjct: 10 DLLVIGGGAAGLTAAAGAARFGARVVLAEREPALGGDCLHHGCVPSKTLLATARARHVMR 69 Query: 64 GAEGFGLKAKPELDLKKLGAWRDGVVKKLTGGVAGLLK--------GNKVELLRGFARFK 115 A FGL A PEL+ A V +++ A + + G V++ G ARF Sbjct: 70 RAALFGLPA-PELEPVDFAA----VARRIREVQAVIQRHDSPQRFTGLGVDVRFGPARFC 124 Query: 116 GPREIEVNGETYGAQSFIIATGSEPM--PLKGF---PFGEDVWDSTRALRVEEGIPKRLL 170 +E+ G A +IATGS P PL G PF + R + + +P LL Sbjct: 125 DEHTVEIGGRRVSAARILIATGSSPQLPPLPGLDTVPFL-----TNRDIFSLDALPASLL 179 Query: 171 VIGGGAVGLELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTK- 229 V+GGG + E+ Q + RLGS VT++ P ILP D + A ++ +L +G++V G Sbjct: 180 VLGGGPMACEMAQAFARLGSRVTMVLRGPRILPRDDADMAGVVHASLAADGVRVLAGATV 239 Query: 230 ---------------------AVGYEKKQDGLHVLLEAAQGGSQEEIVV--DKILVAVGR 266 A G + G+ LE QG + +VV D++L A+GR Sbjct: 240 KMLRAVSAISGRFGKPGEPVGADGNDAAGTGVEAELEVPQGEGRGPLVVRADRLLAALGR 299 Query: 267 RPRTEGLGLEKAGVKVDERGFIQVNARMETSAPGVYAIGDVARPPLLAHKAMKEGLVAAE 326 P T GL L AGV G I V+ RM TS P V+A GDV H A E V Sbjct: 300 TPETAGLDLAAAGVATGRHGGITVDGRMRTSQPHVFAAGDVTGDWQFTHAAGHEAGVVVA 359 Query: 327 NAAGK--NALFDFQVPSVVYTGPEWAGVGLTEEEARKAGYNVKVGKFPFSASGRALTLGG 384 NA + ++P +T PE A VG E A + G V V PF+A+ RAL G Sbjct: 360 NAVLRLPRRADHARMPWCTFTDPELASVGCNERMAAERGLPVDVHVEPFAANDRALAEGT 419 Query: 385 AEGLIKVVGDAETDLLLGVFVVGPQAGELIAEATLALEMGATVSDLGLTIHPHPTLSEGL 444 EG +K+V + +LGV VGP AGE++ E L G +S L +HP+PTL E Sbjct: 420 PEGRLKLVLRKGGNRVLGVQAVGPHAGEVLNEWVAVLGGGVRLSALAGAVHPYPTLGEIS 479 Query: 445 MEAA 448 AA Sbjct: 480 ARAA 483 Lambda K H 0.316 0.138 0.395 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: 612 Number of extensions: 34 Number of successful extensions: 7 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: 461 Length of database: 508 Length adjustment: 34 Effective length of query: 427 Effective length of database: 474 Effective search space: 202398 Effective search space used: 202398 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: 52 (24.6 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