Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate PfGW456L13_2924 Glutathione reductase (EC 1.8.1.7)
Query= SwissProt::P85207 (461 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2924 Length = 452 Score = 251 bits (640), Expect = 5e-71 Identities = 162/445 (36%), Positives = 241/445 (54%), Gaps = 14/445 (3%) Query: 4 YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63 +DL VIG G GG AA A G KV E+ +GG C+NVGC+P K L++ A + Sbjct: 5 FDLYVIGAGSGGVRAARFAAGFGAKVAVAESRYLGGTCVNVGCVPKKLLVYGAHFAEDFE 64 Query: 64 GAEGFGLKA-KPELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGPREIEV 122 A GFG + + D L A +D + +L G LL + V L G A+ P ++E+ Sbjct: 65 QASGFGWGLDEAQFDWPTLIANKDREINRLNGIYRNLLVNSGVTLHEGHAKIVDPHQVEI 124 Query: 123 NGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGAVGLELG 182 NGE + A++ +IATG P + P E S +A ++E +PKR+LV+GGG + +E Sbjct: 125 NGERFTARNILIATGGWPQ-IPEIPGHEHAISSNQAFFLKE-LPKRVLVVGGGYIAVEFA 182 Query: 183 QIYHRLGSEVTLIEYMPEILPAG-DRETAALLRKALEKEGLKVRTGTKAVGYEKKQDG-L 240 I+H LG++ TL+ Y E+ G D L++ L K G+ ++ +K DG L Sbjct: 183 GIFHGLGAKTTLL-YRGELFLRGFDGSVRKHLQEELTKRGMDLQFNADIERIDKLADGSL 241 Query: 241 HVLLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAPG 300 V L+ + ++ D + A GRRP + LGLE GVK+D +GF++V+ +T+ P Sbjct: 242 KVTLKDGR-----QLEADCVFYATGRRPMLDNLGLENTGVKLDRKGFVEVDELYQTAEPS 296 Query: 301 VYAIGDVARPPLLAHKAMKEGLVAAENAAGKNAL--FDFQ-VPSVVYTGPEWAGVGLTEE 357 + A+GDV L A+ EG+ A D++ +P+ V++ P VGLTEE Sbjct: 297 ILALGDVIGRVQLTPVALAEGMAVARRLFKPEQYRPVDYKMIPTAVFSLPNIGTVGLTEE 356 Query: 358 EARKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEA 417 EAR+AG+ V+V + F LT L+K+V DA TD +LG +VGP+AGE++ Sbjct: 357 EAREAGHEVQVFESRFRPMKLTLTECQERTLMKLVVDANTDKVLGCHMVGPEAGEIVQGL 416 Query: 418 TLALEMGATVSDLGLTIHPHPTLSE 442 +AL+ GAT D TI HPT +E Sbjct: 417 AIALKAGATKRDFDETIGVHPTAAE 441 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: 514 Number of extensions: 25 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: 452 Length adjustment: 33 Effective length of query: 428 Effective length of database: 419 Effective search space: 179332 Effective search space used: 179332 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