Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate BPHYT_RS03515 BPHYT_RS03515 D-lactate dehydrogenase
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__BFirm:BPHYT_RS03515 Length = 471 Score = 501 bits (1290), Expect = e-146 Identities = 241/440 (54%), Positives = 319/440 (72%), Gaps = 3/440 (0%) Query: 48 VSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEG 107 VSV VR HGRDES + PD VVF R+ E+V + K+C Y +PIIP+G G+ LEG Sbjct: 30 VSVSEVVRTHHGRDESPFDPQLPDAVVFARTTEDVQTIVKLCGQYNVPIIPYGNGSSLEG 89 Query: 108 GVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGADAS 167 + A+QGGV L +M +V+ ++ ED VTVEPG++RK LN LRDTGL+FP+DPGADAS Sbjct: 90 HLLAVQGGVSIDLSEMNRVLSINAEDLTVTVEPGISRKQLNEALRDTGLFFPIDPGADAS 149 Query: 168 LCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFV 227 + GM+AT ASGTNAVRYGTMRENVL L VVLADG ++ T G R RK++AGY+LT +FV Sbjct: 150 IGGMSATRASGTNAVRYGTMRENVLGLTVVLADGRVIKT---GTRARKSSAGYDLTRMFV 206 Query: 228 GSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVM 287 GSEGTLG+IT+ T+RLY PE++ +AVC+FPS+ +AV + ++ +Q GVPIAR+EF+D + Sbjct: 207 GSEGTLGVITEITVRLYPQPEAVSAAVCAFPSMGAAVRAVIETIQMGVPIARVEFVDSLA 266 Query: 288 INACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRSRL 347 I + NR +NL+ PTLF EFHG+ ++EQ + +EI N G F WA E RSRL Sbjct: 267 IRSINRHSNLTLREAPTLFFEFHGTEAGVKEQAELVQEIAAQNAGEGFEWATRPEDRSRL 326 Query: 348 WKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPIAGHVGDGN 407 W ARH+A++A + L+PGC+A +TDVCVPISRL + + ET+ DL ++ + PI GHVGDGN Sbjct: 327 WNARHNAYFAMLQLKPGCRAVTTDVCVPISRLAECVEETEQDLQASPLPCPIVGHVGDGN 386 Query: 408 FHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLAIE 467 FH I++DPN +E+ R+ +RAL MDGTCTGEHG+GL K L EE G +A++ Sbjct: 387 FHVAILIDPNKPEELVEAERLNHRIVQRALRMDGTCTGEHGVGLHKMGFLLEEHGEVAVD 446 Query: 468 VMKGLKASLDPRNLMNPGKV 487 M+ +K +LDP NLMNPGK+ Sbjct: 447 TMRSIKHALDPHNLMNPGKI 466 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: 594 Number of extensions: 20 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: 471 Length adjustment: 34 Effective length of query: 463 Effective length of database: 437 Effective search space: 202331 Effective search space used: 202331 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