Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate N515DRAFT_2310 N515DRAFT_2310 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component
Query= SwissProt::P85207 (461 letters) >FitnessBrowser__Dyella79:N515DRAFT_2310 Length = 456 Score = 230 bits (586), Expect = 8e-65 Identities = 148/454 (32%), Positives = 233/454 (51%), Gaps = 9/454 (1%) Query: 4 YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63 +D +VIG G G P A R + G +V +E VGG C+N GCIPTKA++ +A H Sbjct: 5 FDAVVIGAGQAGPPLAERLGKAGRRVAVIERKLVGGTCVNTGCIPTKAMVASAYVAHMAG 64 Query: 64 GAEGFGLKAKPE--LDLKKLGAWRDGVVKKLTGGVAGLLKGN-KVELLRGFARFKGPREI 120 A +G++ + +D++++ G+ K GV L G V LLRG ARF+ P + Sbjct: 65 RAHEYGVRGSEDTRVDMQRVWERTQGISGKARSGVEQWLVGMPNVTLLRGHARFESPTTL 124 Query: 121 EVNGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVE-EGIPKRLLVIGGGAVGL 179 + A+SF I G + FP DV T +E +P+ L+++GG +GL Sbjct: 125 RFGEDLIEAESFFINVGGRAS-VPDFPGIHDVPFLTNTGMMELRELPEHLMIVGGSYIGL 183 Query: 180 ELGQIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQDG 239 E GQ++ R GS+VT++E LP D + A + L EG+ V G + + E K Sbjct: 184 EFGQMFRRFGSKVTIVERSQRFLPREDADVADAVLAMLRDEGITVHLGAECIALEGKAGA 243 Query: 240 LHVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAP 299 + + Q E+ V +L+AVGR+P T+ LGL++AGV +DERG I+V+ +S P Sbjct: 244 IRIKARGNQ--LCEQAVGTHLLLAVGRQPNTDDLGLDRAGVALDERGNIKVDDHGRSSVP 301 Query: 300 GVYAIGDVARPPLLAHKAMKEGLVAAENAAGKNAL-FDFQVPSV-VYTGPEWAGVGLTEE 357 ++A+GD H + + + A+ G+ ++ + ++T P A +G++E+ Sbjct: 302 HIWAMGDCNGKGAFTHTSYNDFEIVADAVLGQGRRRISGRIQAYSLFTDPPLARIGMSEQ 361 Query: 358 EARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEA 417 EARK+G V VG P + GRA+ G G +KVV D + LLG + G E I Sbjct: 362 EARKSGREVLVGTRPMARVGRAVERGETVGFMKVVVDGASKELLGAAIFGVNGDEAIHCL 421 Query: 418 TLALEMGATVSDLGLTIHPHPTLSEGLMEAAEAL 451 + A + + +H HPT++E L ++L Sbjct: 422 LDTMYAKAPYTTVSEAVHIHPTVAELLPTTLQSL 455 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: 523 Number of extensions: 24 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: 461 Length of database: 456 Length adjustment: 33 Effective length of query: 428 Effective length of database: 423 Effective search space: 181044 Effective search space used: 181044 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