Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate WP_086511792.1 BZY95_RS20765 glycolate oxidase subunit GlcD
Query= BRENDA::O29853 (443 letters) >NCBI__GCF_002151265.1:WP_086511792.1 Length = 501 Score = 198 bits (503), Expect = 4e-55 Identities = 132/417 (31%), Positives = 214/417 (51%), Gaps = 20/417 (4%) Query: 38 VVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEKMTE-LEVDA 96 +V P + ++V +L + +PV RG GTGLS GA+P G++L + + LE+D Sbjct: 58 LVALPDSLDQVQRLLVECHRLGVPVVTRGAGTGLSAGALPLTHGVLLVMSRFSRILEIDP 117 Query: 97 DNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRN 155 + R+A GV + +AA +GL + P P ++ A ++GG +A NAGGV LKYG + Sbjct: 118 EARIARVEPGVRNLAISEAASPYGLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVH 177 Query: 156 YVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTV 215 V+ +E + +G + +G + ++ G+ LL L GSEG L V+T+ T++L P+ V Sbjct: 178 NVIKVEVLTIEGERMTLGSDAL-DAPGFDLLALFNGSEGMLGVVTEITVKLLPKPEVAKV 236 Query: 216 LAIPFPTMEDAMNCV-VEVARKMLPMALEFMEKRAVEIGEKVSGERWVSREGEAHLLMVF 274 L F +E A N V +A ++P LE M+K A+ E G + + EA LL Sbjct: 237 LMASFDDVEKAGNAVGAIIAAGIIPGGLEMMDKLAIIAAEDFIGAGY-PVDAEAILLCEL 295 Query: 275 ESF-----DEAEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIYE--GLRKEVIEVLD 327 + D+ E ++ + GA + A ++ R R + G +D Sbjct: 296 DGVEADVDDDCETVRQVLEKAGATGIRQARDDAERARFWAGRKNAFPAVGRMSPDYYCMD 355 Query: 328 ACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLVY-----EGWEKSYFEFR 382 +P ++A + ++L+E YG+++ HAGDGN+ HPL+ EG Sbjct: 356 GTIPRRELARVLKGISDLSERYGLKVANVFHAGDGNM--HPLILFDANREGELAVAEALG 413 Query: 383 KSLLSLAVSLGGVISGEHGIGAVKLSELEELF-PEQFELMRQIKLLFDPKNILNPGK 438 +L L V +GG I+GEHG+G K++++ F P++ R K FDP ++LNPGK Sbjct: 414 GEILELCVEVGGTITGEHGVGREKINQMCAQFRPDELATFRAAKAAFDPHDLLNPGK 470 Lambda K H 0.317 0.136 0.388 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: 531 Number of extensions: 24 Number of successful extensions: 7 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: 443 Length of database: 501 Length adjustment: 33 Effective length of query: 410 Effective length of database: 468 Effective search space: 191880 Effective search space used: 191880 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