Align Probable D-lactate dehydrogenase, mitochondrial; DLD; Lactate dehydrogenase D; EC 1.1.2.4 (characterized)
to candidate WP_092483962.1 BM299_RS10985 FAD-linked oxidase C-terminal domain-containing protein
Query= SwissProt::Q7TNG8 (484 letters) >NCBI__GCF_900115975.1:WP_092483962.1 Length = 458 Score = 276 bits (707), Expect = 8e-79 Identities = 162/461 (35%), Positives = 246/461 (53%), Gaps = 10/461 (2%) Query: 27 LSQDFVEALKAVVGSPHVSTASAVREQHGHDESMHRCQPPDAVVWPQNVDQVSRVASLCY 86 + +D V+ +K+VVGS +V + R + +D + R P VV P N +V+ + L Sbjct: 1 MDKDTVKKIKSVVGSEYVLESPEERICYSYDGTARRGIPA-LVVLPGNAREVAEIVRLAN 59 Query: 87 NQGVPIIPFGTGTGVEGGVCAVQGGVCINLTHMDQITELNTEDFSVVVEPGVTRKALNTH 146 +G PI P G GTG+ GG + G+ + L+ M++I E++ +D VVEPGV L+ Sbjct: 60 EKGFPIFPRGAGTGLSGGSVPAEQGLAMVLSRMNRILEISRDDLLAVVEPGVVTGRLHRA 119 Query: 147 LRDSGLWFPVDPGA--DASLCGMAATGASGTNAVRYGTMRDNVINLEVVLPDGRLLHTAG 204 + GL++P DP + ++ G A A G A +YG RD V+ LEVV P G +++T G Sbjct: 120 VEKEGLFYPPDPSSLQTCTIGGNVAENAGGPRAFKYGVTRDYVLGLEVVTPTGEIINTGG 179 Query: 205 RGRHYRKSAAGYNLTGLFVGSEGTLGIITSTTLRLHPAPEATVAATCAFPSVQAAVDSTV 264 R K+ GY+LTGL GSEGTLGIIT TLRL P P A A + V+ A + Sbjct: 180 RTV---KNVTGYDLTGLLTGSEGTLGIITRITLRLVPKPRAVQTALAVYNRVEDAASTVT 236 Query: 265 QILQAAVPVARIEFLDDVMMDACNRHSKLNCPV--APTLFLEFHGSQQTLAEQLQRTEAI 322 +++ + A +E +D + + + +L P+ L +E G +AE+++ E Sbjct: 237 AMIRRGIIPATLELMDRITIRCVENYLRLGLPMDAGAILLIEVDGLPAQVAEEMKLVEDA 296 Query: 323 TQDNGGSHFSWAKEAEKRNELWAARHNAWYAALALSPGSKAYSTDVCVPISRLPEILVET 382 + N A +A +R LW AR A + + P S D VP S++PE++ Sbjct: 297 CRQNSCRALQTATDAAERERLWKARRAVSTAIVQIKPTK--ISEDATVPRSKIPEMVERL 354 Query: 383 KEEIKASKLTGAIVGHVGDGNFHCILLVDPDDAEEQRRVKAFAENLGRRALALGGTCTGE 442 K + L + GH GDGN H +LVD D E + + + + R AL LGGT +GE Sbjct: 355 KSIGEKYGLHLPVFGHAGDGNLHPNILVDKRDPVEMEKAEKAVQEIFRAALDLGGTLSGE 414 Query: 443 HGIGLGKRQLLQEEVGPVGVETMRQLKNTLDPRGLMNPGKV 483 HG+GL K+ L+ E G G+E M+ +K +DPR ++NPGK+ Sbjct: 415 HGVGLLKKPYLEWEAGAGGIEYMKAIKKAVDPRNVLNPGKI 455 Lambda K H 0.318 0.133 0.403 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: 543 Number of extensions: 22 Number of successful extensions: 5 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: 484 Length of database: 458 Length adjustment: 33 Effective length of query: 451 Effective length of database: 425 Effective search space: 191675 Effective search space used: 191675 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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