Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate 17057 b2979 glycolate oxidase subunit, FAD-linked (NCBI)
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__Keio:17057 Length = 499 Score = 199 bits (505), Expect = 2e-55 Identities = 131/433 (30%), Positives = 210/433 (48%), Gaps = 21/433 (4%) Query: 63 SVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEGGVGALQGGVCFSLRK 122 S +R RP +VV P+ +E+V+A+ +CH R+P++ G GTGL GG L+ GV + + Sbjct: 50 SAYRTRPL-LVVLPKQMEQVTAILAVCHRLRVPVVTRGAGTGLSGGALPLEKGVLLVMAR 108 Query: 123 MEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGAD--ASLCGMAATSASGTN 180 ++++D++ V+PGV +++ + L++ DP + S+ G A +A G + Sbjct: 109 FKEILDINPVGRRARVQPGVRNLAISQAVAPHNLYYAPDPSSQIACSIGGNVAENAGGVH 168 Query: 181 AVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFVGSEGTLGIITKAT 240 ++YG N+L +EV DG L T G + G++L LF GSEG LG+ T+ T Sbjct: 169 CLKYGLTVHNLLKIEVQTLDGEAL-TLGS---DALDSPGFDLLALFTGSEGMLGVTTEVT 224 Query: 241 LRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVMINACNRFNNLSYA 300 ++L P + SF SV+ A + I+ G+ +E +D++ I A F + Y Sbjct: 225 VKLLPKPPVARVLLASFDSVEKAGLAVGDIIANGIIPGGLEMMDNLSIRAAEDFIHAGYP 284 Query: 301 V--TPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRSRLWKARHDAWYAA 358 V L E G ++E +I G +D A+DE R R W R +A+ A Sbjct: 285 VDAEAILLCELDGVESDVQEDCERVNDILLKAGATDVRLAQDEAERVRFWAGRKNAFPAV 344 Query: 359 MALRPGCKAYSTDVCVPISRLPQII-----VETKADLISNNITGPIAGHVGDGNFHCLIV 413 + P Y D +P LP ++ + + DL N+ H GDGN H LI+ Sbjct: 345 GRISP--DYYCMDGTIPRRALPGVLEGIARLSQQYDLRVANVF-----HAGDGNMHPLIL 397 Query: 414 LDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLAIEVMKGLK 473 D N+ E R ++ + + G+ +GEHGIG K + + I +K Sbjct: 398 FDANEPGEFARAEELGGKILELCVEVGGSISGEHGIGREKINQMCAQFNSDEITTFHAVK 457 Query: 474 ASLDPRNLMNPGK 486 A+ DP L+NPGK Sbjct: 458 AAFDPDGLLNPGK 470 Lambda K H 0.319 0.135 0.399 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: 558 Number of extensions: 27 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: 497 Length of database: 499 Length adjustment: 34 Effective length of query: 463 Effective length of database: 465 Effective search space: 215295 Effective search space used: 215295 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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