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 PfGW456L13_944 D-2-hydroxyglutarate dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_944 Length = 472 Score = 288 bits (737), Expect = 3e-82 Identities = 163/465 (35%), Positives = 261/465 (56%), Gaps = 21/465 (4%) Query: 70 KSILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVV 129 K+++ ++L ++++ L+ Y +DW + + ++ PK+ E+V I+ + N K+A+V Sbjct: 19 KTLVEPGKVL--TDADSLNAYGKDWTKHFAPAPTAIVFPKTTEQVQAIVLWANKHKVALV 76 Query: 130 PQGGNTGLVGGSVPIFDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYM 189 P GG TGL +V E+++S +N+I D + C GV+ E+ N E Sbjct: 77 PSGGRTGLSAAAVAANGEVVVSFDYMNQILDVNLTDRTAVCQPGVVTEHLQNVAEENGLY 136 Query: 190 FPLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNT 249 +P+D + GS +GG + TNAGG++++RYG V G++VV G ++ + K+ T Sbjct: 137 YPVDFASAGSSQIGGNIGTNAGGIKVIRYGMTRNWVAGMKVVTGKGDVLELNRDLIKNAT 196 Query: 250 GYDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEIL 309 GYD++QLFIG+EGT+G + ++ PK L F+ + V + +L L Sbjct: 197 GYDMRQLFIGAEGTLGFVVEATMRLDRAPKNLTAMVLGTADFDSIMPVLHAFQSKLD--L 254 Query: 310 SAFEFMDAKSQVLAKSQLK-DAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEE 368 +AFEF K+ LAK + D P E + PFY L+E + ++ + LETF E+ +E+ Sbjct: 255 TAFEFFSDKA--LAKVMARGDVPAPFESDCPFYALLEFEATTEEVANHALETF-EHCVEQ 311 Query: 369 GIVTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSE 428 G V DGV++Q ET+LQNLWK RE I E + ++ YK D+S+ V A L E Sbjct: 312 GWVLDGVMSQSETQLQNLWKLREYISE-TISHWTPYKNDISV-------TVSKVPAFLKE 363 Query: 429 AELVGDSPKPVVGAIGYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHG 483 + + P + +GH+GDGNLHLN+ + E T+ +V+E V +G Sbjct: 364 IDAIVGEHYPDFEIVWFGHIGDGNLHLNILKPDNLSKDEFFAKCATVNKWVFETVEKYNG 423 Query: 484 SVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528 S+SAEHG+G K++Y+ YS+SP E++ MK +K +DPNGI+NP K Sbjct: 424 SISAEHGVGMTKRDYLTYSRSPVEIEYMKAVKAVFDPNGIMNPGK 468 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: 551 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: 530 Length of database: 472 Length adjustment: 34 Effective length of query: 496 Effective length of database: 438 Effective search space: 217248 Effective search space used: 217248 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