Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate 3607953 Dshi_1361 D-lactate dehydrogenase (cytochrome) (RefSeq)
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__Dino:3607953 Length = 468 Score = 451 bits (1161), Expect = e-131 Identities = 224/442 (50%), Positives = 297/442 (67%), Gaps = 3/442 (0%) Query: 48 VSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEG 107 + G+A+REQHG + +PPD V PR EV + +IC Y +P++PFGTGT LEG Sbjct: 29 LQTGAALREQHGHTTTWLPNQPPDAVFLPRETAEVQDVLRICTAYGMPLVPFGTGTSLEG 88 Query: 108 GVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGADAS 167 V A GG+ +M QV+ +H ED D V+PG+TRK+LN LR TGL+FPVDPGADAS Sbjct: 89 HVNAPLGGLSLDFAEMNQVLAIHPEDMDCVVQPGITRKALNEELRATGLFFPVDPGADAS 148 Query: 168 LCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFV 227 L GMAAT ASGTNAVRYGTMR+ VL LE V ADG ++ TA +R RKT+AGY+LT L V Sbjct: 149 LGGMAATRASGTNAVRYGTMRDVVLALEAVTADGRVIRTA---KRARKTSAGYDLTRLLV 205 Query: 228 GSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVM 287 GSEGTLG+IT+ TL+L G+PE++ A CSF SV++A + + +Q GVP+ARIEFLD + Sbjct: 206 GSEGTLGVITELTLKLSGIPEAVAGATCSFASVEAACAAVIATIQYGVPVARIEFLDALS 265 Query: 288 INACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRSRL 347 + + N ++ LS P L LEFHGS + EQ EI D+G F W D E R+++ Sbjct: 266 VRSINAYSKLSLPEAPLLLLEFHGSEAGVAEQSETFGEIAADHGALAFDWTSDAEARAKM 325 Query: 348 WKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPIAGHVGDGN 407 W+ARHDA++A ALRPG A+ TDVCVP+SRL + + ++ I P GHVGDGN Sbjct: 326 WQARHDAYWAMRALRPGFDAFVTDVCVPVSRLAEAVSAAAERAEADGIIAPTLGHVGDGN 385 Query: 408 FHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLAIE 467 FH +++DP+D R S+ L A+++DGTCTGEHGIG GK L E+G ++ Sbjct: 386 FHVALLIDPDDPGGRARAESYIGWLNDLAISLDGTCTGEHGIGQGKVKYLARELGANTVD 445 Query: 468 VMKGLKASLDPRNLMNPGKVLE 489 VM LK+++DP N++NPGK+ + Sbjct: 446 VMAALKSAMDPDNILNPGKLFQ 467 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: 556 Number of extensions: 18 Number of successful extensions: 2 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: 468 Length adjustment: 34 Effective length of query: 463 Effective length of database: 434 Effective search space: 200942 Effective search space used: 200942 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