Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate RR42_RS17285 RR42_RS17285 2-hydroxy-acid oxidase
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__Cup4G11:RR42_RS17285 Length = 472 Score = 476 bits (1225), Expect = e-139 Identities = 232/442 (52%), Positives = 311/442 (70%), Gaps = 3/442 (0%) Query: 46 EGVSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAKICHHYRLPIIPFGTGTGL 105 E S V + HGRDES PD VVF + EEV+ +A++C+ +R+P+I +G G+ L Sbjct: 29 ERFSTSPGVCDHHGRDESPFPPAAPDGVVFAHTTEEVAEVARLCNEHRVPLIAYGAGSSL 88 Query: 106 EGGVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSLNSYLRDTGLWFPVDPGAD 165 EG + A+ GG+ L +M +V+ + ED +VTV+PGVTRK LN ++D+GL+FP+DPGAD Sbjct: 89 EGHLLAVAGGISLDLSEMNKVLSVQPEDLNVTVQPGVTRKQLNQEIKDSGLFFPIDPGAD 148 Query: 166 ASLCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTAGKGRRPRKTAAGYNLTNL 225 ASL GM AT ASGTNAVRYGTMRENVL L VV ADG I+ T G RK++AGY+LT L Sbjct: 149 ASLGGMCATRASGTNAVRYGTMRENVLALTVVTADGRIIKT---GTHARKSSAGYDLTRL 205 Query: 226 FVGSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDSTVQILQAGVPIARIEFLDD 285 +GSEGTLGIIT+ T+RLY PE++ +A+CSFPS+ SAV +T++ +Q GVP+AR+EF+D Sbjct: 206 MIGSEGTLGIITEVTVRLYPQPEAISAAICSFPSMGSAVRATIETIQLGVPVARVEFVDA 265 Query: 286 VMINACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEITRDNGGSDFAWAEDEETRS 345 + I A NR +NLS P LF EFHG+ ++EQ ++I DNGG F WA E RS Sbjct: 266 LAIRAINRHDNLSMPEAPHLFFEFHGTEAGVKEQAETVQQIAADNGGQGFEWATRPEDRS 325 Query: 346 RLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETKADLISNNITGPIAGHVGD 405 RLW ARH A++A + L+PGCKA +TDVCVPISRL + ET+ DL ++++ PI GHVGD Sbjct: 326 RLWNARHTAYFAMLQLKPGCKAVTTDVCVPISRLADCVTETERDLNASSLPCPIVGHVGD 385 Query: 406 GNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEHGIGLGKRALLREEVGPLA 465 GNFH I+ DP +E+ + R+ RALAM GTCTGEHG+GL K L E G A Sbjct: 386 GNFHVAILTDPEKPEELAEAETINRRIVERALAMGGTCTGEHGVGLHKMDFLVSEHGEDA 445 Query: 466 IEVMKGLKASLDPRNLMNPGKV 487 +++M+ +K +LDP +++NPGK+ Sbjct: 446 LDLMRAIKNALDPNHILNPGKI 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: 628 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: 472 Length adjustment: 34 Effective length of query: 463 Effective length of database: 438 Effective search space: 202794 Effective search space used: 202794 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