Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate AZOBR_RS12240 AZOBR_RS12240 2-hydroxy-acid oxidase
Query= SwissProt::F1QXM5 (497 letters) >FitnessBrowser__azobra:AZOBR_RS12240 Length = 467 Score = 531 bits (1368), Expect = e-155 Identities = 261/463 (56%), Positives = 336/463 (72%), Gaps = 5/463 (1%) Query: 28 KTAAVERVVSSFRSVTGDEGVSVGSAVREQHGRDESVHRCRPPDVVVFPRSVEEVSALAK 87 + A + + + F+++ GD + +AVRE HG+DES H PPD V F S EEVSA+ Sbjct: 10 RVAFTDEMKAEFKALLGDR-FTTAAAVREHHGKDESYHPNFPPDGVAFATSTEEVSAIVT 68 Query: 88 ICHHYRLPIIPFGTGTGLEGGVGALQGGVCFSLRKMEQVVDLHQEDFDVTVEPGVTRKSL 147 +C ++LPIIPFGTGT LEGGV AL GGVC + M++V+ + ED DVTV+ GVTRK L Sbjct: 69 LCAKHKLPIIPFGTGTSLEGGVAALAGGVCIDVSNMKEVLRVSPEDLDVTVQAGVTRKQL 128 Query: 148 NSYLRDTGLWFPVDPGADASLCGMAATSASGTNAVRYGTMRENVLNLEVVLADGTILHTA 207 N +LRDTGL+FP+DPGADASL GMA+T ASGTNAVRYGTMRENVL L VVLADG I+ T Sbjct: 129 NEHLRDTGLFFPIDPGADASLGGMASTRASGTNAVRYGTMRENVLGLTVVLADGRIIKTG 188 Query: 208 GKGRRPRKTAAGYNLTNLFVGSEGTLGIITKATLRLYGVPESMVSAVCSFPSVQSAVDST 267 G R RK+AAGY+LT LFVG+EGTLGIIT+ TLRLYG+PE++ SAVC F ++ AVD+ Sbjct: 189 G---RARKSAAGYDLTRLFVGAEGTLGIITEVTLRLYGIPEAISSAVCPFNDIRGAVDTV 245 Query: 268 VQILQAGVPIARIEFLDDVMINACNRFNNLSYAVTPTLFLEFHGSSKSMEEQVSVTEEIT 327 +Q +Q+G+P+ARIE LD+V ++A N+++ L Y V PTLF EFHG++ ++EQ + I Sbjct: 246 IQTIQSGIPVARIELLDEVQMDAVNKYSKLDYKVAPTLFFEFHGTAAGVKEQAEMVAAIA 305 Query: 328 RDNGGSDFAWAEDEETRSRLWKARHDAWYAAMALRPGCKAYSTDVCVPISRLPQIIVETK 387 + GGS+F WA E RS+LW+ARHD +YAA+ALRPG K + TDVCVPISRL I+ETK Sbjct: 306 AEFGGSEFTWATRPEDRSKLWQARHDGYYAALALRPGSKGWPTDVCVPISRLADCILETK 365 Query: 388 ADLISNNITGPIAGHVGDGNFHCLIVLDPNDTDEVQRVHSFTERLARRALAMDGTCTGEH 447 D+ +++ P+ GHVGDGNFH + V+DP+ +E+ +R+ RALAM GTCTGEH Sbjct: 366 KDIAESSMLAPLVGHVGDGNFHLVYVIDPDKPEELAEAKRLNDRMVDRALAMGGTCTGEH 425 Query: 448 GIGLGKRALLREEVGPLAIEVMKGLKASLDPRNLMNPGKVLEL 490 GIG GK L +E G A VM LK + DP N MNPGKV+ + Sbjct: 426 GIGYGKMEFLEKEAGD-AFAVMGELKRAFDPENRMNPGKVVRI 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: 594 Number of extensions: 23 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