Align D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 (characterized)
to candidate PP_5154 PP_5154 putative Oxidoreductase, FAD-binding
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Putida:PP_5154 Length = 455 Score = 293 bits (750), Expect = 9e-84 Identities = 160/449 (35%), Positives = 256/449 (57%), Gaps = 21/449 (4%) Query: 87 LSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFD 146 L Y +DW + Y ++ PK++E+V I+++ N K+A+VP GG TGL G+V Sbjct: 16 LEAYGKDWTKHYPPAPSAIVFPKTIEQVQAIVHWANAHKVALVPSGGRTGLSAGAVAANG 75 Query: 147 ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVV 206 E++++ +N+I F+ + C GV+ Y EQ +P+D + GS +GG + Sbjct: 76 EVVVAFDYMNQILGFNAFDRTVVCQPGVVTRQLQTYAEEQGLYYPVDFASSGSSQIGGNI 135 Query: 207 ATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGI 266 TNAGG++++RYG V GL+VV G+++ + K+ TGYDL+QLFIG+EGT+G Sbjct: 136 GTNAGGIKVIRYGMTRNWVAGLKVVTGKGELLELNKDLIKNATGYDLRQLFIGAEGTLGF 195 Query: 267 ITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAK--SQVLAK 324 + ++ P+ L F+ + V + +L L+AFEF K +++LA+ Sbjct: 196 VVEATMRLDRAPRNLTAMVLGTPDFDSIMPVLHAFQGKLD--LTAFEFFSDKGLAKILAR 253 Query: 325 SQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQ 384 D P + PFY L+E S +D + L TF E+ +E+G V DGV++Q E++L+ Sbjct: 254 G---DVPAPFATDCPFYALLEFEASTEDVANEALATF-EHCVEQGWVLDGVMSQSESQLK 309 Query: 385 NLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIG 444 NLWK RE + E + ++ YK D+S+ + + + + +A +SE P + Sbjct: 310 NLWKLREYLSE-TISHWTPYKNDISVTVSKVPAFLRDIDAIVSE-------HYPDYEVVW 361 Query: 445 YGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYI 499 YGH+GDGNLHLN+ E+ + + +V+E V +GS+SAEHG+G K++Y+ Sbjct: 362 YGHIGDGNLHLNILKPEHMSKDDFFASCAKVNKWVFEIVERYNGSISAEHGVGMTKRDYL 421 Query: 500 GYSKSPEEVKMMKDLKVHYDPNGILNPYK 528 GYS+SPEE+ MK +K +DPNGI+NP K Sbjct: 422 GYSRSPEEIACMKAIKAVFDPNGIMNPGK 450 Lambda K H 0.316 0.135 0.385 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: 538 Number of extensions: 22 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: 530 Length of database: 455 Length adjustment: 34 Effective length of query: 496 Effective length of database: 421 Effective search space: 208816 Effective search space used: 208816 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