Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; EC 1.8.1.4 (characterized)
to candidate PP_3819 PP_3819 glutathione reductase (NADPH)
Query= SwissProt::P85207 (461 letters) >FitnessBrowser__Putida:PP_3819 Length = 451 Score = 257 bits (657), Expect = 5e-73 Identities = 167/443 (37%), Positives = 242/443 (54%), Gaps = 10/443 (2%) Query: 4 YDLIVIGTGPGGYPAAIRGAQLGLKVLAVEAAEVGGVCLNVGCIPTKALLHAAETVHHLK 63 +DL VIG G GG AA A G KV E+ +GG C+NVGC+P K L++ A L+ Sbjct: 5 FDLFVIGAGSGGVRAARFAAGFGAKVAVAESRYLGGTCVNVGCVPKKLLVYGAHVADELE 64 Query: 64 GAEGFGLKAKP-ELDLKKLGAWRDGVVKKLTGGVAGLLKGNKVELLRGFARFKGPREIEV 122 A GFG + D L A ++ +++L G LL + V LL+G AR G E+EV Sbjct: 65 QAAGFGWTLEEGHFDWGTLIANKNREIERLNGIYRNLLVNSGVTLLQGHARLTGANEVEV 124 Query: 123 NGETYGAQSFIIATGSEPMPLKGFPFGEDVWDSTRALRVEEGIPKRLLVIGGGAVGLELG 182 +G+ Y A+ +IATG P + P E S A +++ +P+R+LV+GGG + +E Sbjct: 125 DGQRYTAEHILIATGGWPQ-VPDIPGKELAITSNEAFYLKD-LPRRVLVVGGGYIAVEFA 182 Query: 183 QIYHRLGSEVTLIEYMPEILPAGDRETAALLRKALEKEGLKVRTGTKAVGYEKKQDGLHV 242 I+ LG++ TL+ L D L++ LEK GL ++ +K +DG Sbjct: 183 GIFQGLGADTTLLYRGDLFLRGFDGSVRTHLKQELEKRGLDLQFNADIQRIDKLEDGR-- 240 Query: 243 LLEAAQGGSQEEIVVDKILVAVGRRPRTEGLGLEKAGVKVDERGFIQVNARMETSAPGVY 302 L + G E+V D + A GRRP + LGLE GV++DERG+I+V+ + +T+AP + Sbjct: 241 LKATLKDG--RELVADCVFYATGRRPMLDNLGLENTGVELDERGYIRVDEQYQTTAPSIL 298 Query: 303 AIGDVARPPLLAHKAMKEGLVAAENAAGKNAL--FDFQ-VPSVVYTGPEWAGVGLTEEEA 359 AIGDV L A+ EG+ A D+Q +P+ V++ P VGLTEE+A Sbjct: 299 AIGDVIGRVQLTPVALAEGMAVARRLFKPEQYRPVDYQNIPTAVFSQPPIGTVGLTEEQA 358 Query: 360 RKAGYNVKVGKFPFSASGRALTLGGAEGLIKVVGDAETDLLLGVFVVGPQAGELIAEATL 419 +AG+ V+V + F A LT + L+K+V DAETD +LG +VGP AGE+I + Sbjct: 359 LEAGHKVQVFESRFRAMKLTLTDIQEKTLMKLVVDAETDKVLGCHMVGPDAGEIIQGLGI 418 Query: 420 ALEMGATVSDLGLTIHPHPTLSE 442 AL+ GAT TI HPT +E Sbjct: 419 ALKAGATKQQFDETIGVHPTAAE 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: 552 Number of extensions: 29 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: 451 Length adjustment: 33 Effective length of query: 428 Effective length of database: 418 Effective search space: 178904 Effective search space used: 178904 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