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 GFF2609 HP15_2553 oxidoreductase, FAD-binding protein
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Marino:GFF2609 Length = 479 Score = 284 bits (727), Expect = 5e-81 Identities = 163/454 (35%), Positives = 251/454 (55%), Gaps = 21/454 (4%) Query: 82 SESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGS 141 ++ DL Y +DW + Y + + PK+ E+V ++ + N+ ++A+VP GG TGL G+ Sbjct: 37 TDPADLDTYGKDWTKIYPPKPLAIALPKTTEQVQALVKFANENQVALVPSGGRTGLSAGA 96 Query: 142 VPIFDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCH 201 V E++++ N+N+I DF+ ++C AGV+ E N + +P+D + GS Sbjct: 97 VAANGEVVVAFDNMNQILDFNASDRTVRCQAGVVTEQLQNCAEDNGLYYPVDFASAGSSQ 156 Query: 202 VGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSE 261 +GG ++TNAGG++++RYG V GL+VV G I++ + K+NTGYDL+ LFIG+E Sbjct: 157 LGGNLSTNAGGIKVIRYGMSRDWVAGLKVVTGKGDILDLNKDLEKNNTGYDLRHLFIGAE 216 Query: 262 GTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFM--DAKS 319 GT+G IT ++ KP V L + + V ++++ L+A+EF A Sbjct: 217 GTLGFITEATMKLSRKPDNLTVLVLGLNDLTNTMDVLQTFQKKID--LTAYEFFSHQAMG 274 Query: 320 QVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQD 379 VLA Q++ P E E P+Y L+E + D + F E +E G V DGV++Q Sbjct: 275 HVLAHGQVQ---APFETEAPYYALLEFESVSDQVMDDAMALF-EQCVENGWVLDGVISQS 330 Query: 380 ETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPV 439 ET+ QNLW+ RE I E S A YK D+S+ +V L E + V P Sbjct: 331 ETQAQNLWQLRERISE-SIAPRTPYKNDISV-------VVSKVPGFLQEIDAVVTEHYPD 382 Query: 440 VGAIGYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHGSVSAEHGLGFQ 494 I +GH+GDGNLHLN+ E N + + + +V+E V GSVSAEHG+G Sbjct: 383 FEIIWFGHIGDGNLHLNILKPEDMANEDFFEKCQQVNKWVFEIVERYQGSVSAEHGVGMT 442 Query: 495 KKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528 KK Y+ Y++S E+ ++ +K +DPNGI+NP K Sbjct: 443 KKPYLQYTRSEAEIAYLRGIKQVFDPNGIMNPGK 476 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: 585 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: 479 Length adjustment: 34 Effective length of query: 496 Effective length of database: 445 Effective search space: 220720 Effective search space used: 220720 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