Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate GFF2781 PGA1_c28240 putative D-lactate dehydrogenase
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__Phaeo:GFF2781 Length = 467 Score = 455 bits (1170), Expect = e-132 Identities = 218/445 (48%), Positives = 309/445 (69%), Gaps = 4/445 (0%) Query: 46 EGVSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGL 105 E + G A+REQHG + +PPD VVFP S +EV+ + + C Y +P+IP+GTGT L Sbjct: 27 EQLQTGQAIREQHGHTTTWITNQPPDAVVFPTSTDEVADIVRTCADYGVPVIPYGTGTSL 86 Query: 106 EGGVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGAD 165 EG V A GG+C + +M++++ +H ED DV V+PGVTR+ LN+YLRD GL+FP+DPGA+ Sbjct: 87 EGHVNAPAGGICVDMMRMDKILAVHAEDLDVVVQPGVTREQLNTYLRDQGLFFPIDPGAN 146 Query: 166 ASLCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNL 225 ASL GMAAT ASGTNAVRYGTM++NVL LE V+ADG ++ TA +R +K++AGY++T L Sbjct: 147 ASLGGMAATRASGTNAVRYGTMKDNVLALEAVMADGGVIRTA---QRAKKSSAGYDMTRL 203 Query: 226 FVGSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDD 285 VGSEGTLG+IT+ TLRL G+PE++ SA C+F SV A + + +Q G+P++RIE LD+ Sbjct: 204 LVGSEGTLGLITELTLRLQGIPEAIRSARCAFRSVDDACRAVMMTIQYGIPVSRIELLDE 263 Query: 286 VMINACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRS 345 + + A N ++ L P L LEFHGS + EQ +I + GG D A E RS Sbjct: 264 MSVRAANAYSGLDLPEMPLLLLEFHGSDAGVVEQADTFAQIAEEFGGFDIAATSTAEERS 323 Query: 346 RLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPIAGHVGD 405 +LW+ARHD ++A++ LRPG K STDVCVPIS+L + + ++ N+ P+ GHVGD Sbjct: 324 KLWQARHDMYWASLQLRPGAKGISTDVCVPISKLAECVSAARSKAEEMNLLAPMVGHVGD 383 Query: 406 GNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLA 465 GNFH L++++ + +E + ++ L A++++GTCTGEHGIG GKR L++E+G Sbjct: 384 GNFHALLLINMDSAEEREAADAYVGWLNELAISIEGTCTGEHGIGQGKRPYLQQELGE-T 442 Query: 466 IEVMKGLKASLDPRNLMNPGKVLEL 490 M +KA+LDP N++NPGK+LE+ Sbjct: 443 TRYMAAIKAALDPENILNPGKILEI 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: 539 Number of extensions: 22 Number of successful extensions: 3 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: 467 Length adjustment: 34 Effective length of query: 463 Effective length of database: 433 Effective search space: 200479 Effective search space used: 200479 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