Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_028585357.1 G494_RS0116210 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::P85207 (461 letters) >NCBI__GCF_000429965.1:WP_028585357.1 Length = 448 Score = 164 bits (416), Expect = 4e-45 Identities = 136/447 (30%), Positives = 204/447 (45%), Gaps = 11/447 (2%) Query: 2 KTYDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHH 61 + +D +V+G+G Y A + G +V ++ GG C GC P K L+ E V Sbjct: 4 QNFDTVVVGSGTSAYFAVDGLLRHGQQVALIDERPFGGTCALRGCQPKKYLVSNVEAVAL 63 Query: 62 LKGAEGFGLKAKPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGPREIE 121 EG GL P+ D + L ++ ++ + V +G A G + Sbjct: 64 ASQLEGQGLTIPPQTDWQALQILKNRFLEGRPEAELRQWQKKGVTTFQGRAVMSGTDRLT 123 Query: 122 VNGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGAVGLEL 181 VN A + ++ATG+ P P + + DS L + + +PKR+L IGGG + E Sbjct: 124 VNNTVLTADNIVLATGAIPRR-STIPGADYLQDSEAFLNLAQ-LPKRILFIGGGYISFEF 181 Query: 182 GQIYHRLGSE-VTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQDGL 240 + R G+E VT++ L + D++ +L A G++V + E G Sbjct: 182 AHVAIRAGAEEVTILHRSALPLKSFDQDCVQVLLTASRALGIRVLLNQEPTAVEMIDSGY 241 Query: 241 HVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAPG 300 L +GG E D I+ A GR P E L + V D RG + S P Sbjct: 242 ---LVHGKGGQSWE--ADCIIEASGRVPNLEVLAGGEGKVDADRRGILVTPYLQSVSNPR 296 Query: 301 VYAIGDVARP-PLLAHKAMKEGLVAAENAAG-KNALFDFQV-PSVVYTGPEWAGVGLTEE 357 VYAIGD A +LA A +EG V N G + D+ V PSVV+T P VGLTE+ Sbjct: 297 VYAIGDCAATGSMLAPVADREGQVVVANILGERQQSIDYAVVPSVVFTIPPMGSVGLTEQ 356 Query: 358 EARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEA 417 +AR+ G + + S +L +G AEG K++ D ETD LLG +V A E+I Sbjct: 357 QAREQGLEFRSRQGSTSRWPSSLRIGEAEGFYKILIDPETDRLLGAHLVRHNATEVINTL 416 Query: 418 TLALEMGATVSDLGLTIHPHPTLSEGL 444 LA++ T ++L + +PT + L Sbjct: 417 ALAMKYQITANELADFMWAYPTSTSDL 443 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: 459 Number of extensions: 25 Number of successful extensions: 4 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: 448 Length adjustment: 33 Effective length of query: 428 Effective length of database: 415 Effective search space: 177620 Effective search space used: 177620 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 24 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