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 SMc00985 SMc00985 oxidoreductase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Smeli:SMc00985 Length = 480 Score = 313 bits (803), Expect = 7e-90 Identities = 169/441 (38%), Positives = 261/441 (59%), Gaps = 15/441 (3%) Query: 98 YKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFD--ELILSLANL 155 Y+G + LVLRP SVE+VSL++ + + AVVPQGGNTG V G +P +++LSL L Sbjct: 41 YRGTTPLVLRPGSVEEVSLVMRLASQTRTAVVPQGGNTGHVAGQIPREGKADVVLSLERL 100 Query: 156 NKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNAGGLRL 215 N+IRD DPV ++ DAG IL + + + +FPL LG++GS +GG ++TNAGG + Sbjct: 101 NRIRDIDPVGNVIVADAGCILADIQKAADDVDRLFPLSLGSEGSARIGGNLSTNAGGTAV 160 Query: 216 LRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGVSILTV 275 L YG++ LGLEVV+P G+I + + +RKDNTGYDL+ LFIG+EGT+G+ITG + Sbjct: 161 LAYGNMRQLCLGLEVVLPTGEIWDGLRRLRKDNTGYDLRDLFIGAEGTLGVITGAVLKLF 220 Query: 276 PKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAKSQLKDAAFPLE 335 PKP+ V++ + S ED +F RA L+ FE M + P+E Sbjct: 221 PKPRGHQVAFAGLRSVEDALTLFDRATSVCGPALTGFELMPRLGIEFTTRHIAGVRDPME 280 Query: 336 DEHPFYILIETSGSN-KDHDDSKLETFLENVMEEGIVTDGVVAQDETELQNLWKWREMIP 394 HP+Y LI+ S S+ + + ++ LE V+ +G+V + V+AQ+E + + LW RE + Sbjct: 281 TTHPWYALIDISTSDTAESAERMVQDLLEAVIADGLVENAVIAQNEAQRRALWHMRESMS 340 Query: 395 EASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVGDGNLH 454 A + GG K+DVS+P V + A ++EA+ + P +GH+GDGN+H Sbjct: 341 PAQKPEGGSIKHDVSVP-------VSSIPAFMTEADALVSKAIPGARICAFGHMGDGNIH 393 Query: 455 LNV-----AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVK 509 N+ A ++ + + + V+ V GS+SAEHG+G K++ + +SP E++ Sbjct: 394 YNISQPVGADKQSFLDRWREINAIVHAVVLKHDGSISAEHGIGQLKRDELAAIRSPIEIE 453 Query: 510 MMKDLKVHYDPNGILNPYKYI 530 +M+ +K +DP GI+NP K + Sbjct: 454 LMRRIKHAFDPAGIMNPDKVL 474 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: 553 Number of extensions: 18 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: 480 Length adjustment: 34 Effective length of query: 496 Effective length of database: 446 Effective search space: 221216 Effective search space used: 221216 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