Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate SMc01455 SMc01455 D-lactate dehydrogenase (cytochrome) protein
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__Smeli:SMc01455 Length = 468 Score = 457 bits (1176), Expect = e-133 Identities = 224/437 (51%), Positives = 302/437 (69%), Gaps = 4/437 (0%) Query: 51 GSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGLEGGVG 110 G A+R QH + + PD VVFP S EV + +I +R+P+IPFGTG+ LEG V Sbjct: 34 GEAIRAQHANTTTYIPAQLPDAVVFPESAAEVREIVEIACEHRVPLIPFGTGSSLEGHVN 93 Query: 111 ALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGADASLCG 170 A GG+ + +M +V+ ++ ED D TVEPGVTR+ LNSYLRDTGL+FP+DPGA+AS+ G Sbjct: 94 APHGGISVDMMRMNRVLAVNAEDLDCTVEPGVTREELNSYLRDTGLFFPIDPGANASIGG 153 Query: 171 MAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNLFVGSE 230 MA+T ASGTNAVRYGTM+ENVL + V+A G + TA R RK++AGY+LT LFVG+E Sbjct: 154 MASTRASGTNAVRYGTMKENVLAVTAVVAGGREIRTA---HRARKSSAGYDLTRLFVGAE 210 Query: 231 GTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDDVMINA 290 GTLGI+T TLRL G+PE + VC FP++ A ++ + +Q+G+P+ARIE LD + + A Sbjct: 211 GTLGIVTSITLRLQGIPEVISGGVCPFPTIADACNAVILTIQSGIPVARIELLDALQMKA 270 Query: 291 CNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRSRLWKA 350 CN ++ L+Y TPTLF+EFHG+ +S+E Q EI + G + F W + E R+RLWKA Sbjct: 271 CNAYSGLTYQETPTLFVEFHGNGESVELQSRQFAEIASEFGSTGFIWTTNPEERARLWKA 330 Query: 351 RHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPIAGHVGDGNFHC 410 RH+A++A +L PG STDVCVPISRL + T D+ ++ + PI GH GDGNFH Sbjct: 331 RHNAYWAQKSLMPGRAILSTDVCVPISRLADCVAATHEDIAAHGLVAPIVGHAGDGNFHV 390 Query: 411 LIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLAIEVMK 470 ++ D D +V + +F ERL RAL+MDGTCTGEHGIG GK L E+G A+++M+ Sbjct: 391 GLLFDDKDAADVAQAEAFVERLNARALSMDGTCTGEHGIGQGKMPFLAAELGD-ALDLMR 449 Query: 471 GLKASLDPRNLMNPGKV 487 +K SLDP N+ NPGK+ Sbjct: 450 QIKRSLDPDNIFNPGKI 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: 564 Number of extensions: 20 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: 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