Align D-lactate dehydrogenase (EC 1.1.1.28); D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate 5209072 Shew_1550 FAD linked oxidase domain-containing protein (RefSeq)
Query= BRENDA::Q9YEU4 (473 letters) >FitnessBrowser__PV4:5209072 Length = 1026 Score = 113 bits (283), Expect = 3e-29 Identities = 131/504 (25%), Positives = 209/504 (41%), Gaps = 85/504 (16%) Query: 39 EAVVFPESAQDVSRLVRYAYS---REVYIYPQGSSTDLAGGAFPERPGVVVSMER-MRRV 94 +AV++P++ DV ++ A ++V +G T G + G+++ + R +V Sbjct: 53 QAVLYPKTQADVKLIMTLATKPEFKQVVFSARGGGTGTNGQSLTH--GLILDLSRYFNQV 110 Query: 95 REVSVLDSVAVVEPGVRLWDLNVELSKYRYMFPIDPGSVKVATVGGAINTGAGGMRGARY 154 E++ + V+ GV LN L + + F D + AT+GG INT A G Y Sbjct: 111 IEINEKERWVRVQAGVVKDALNDALRPHGFFFSPDLSTSNRATMGGMINTDASGAGSLVY 170 Query: 155 GTMRDWVLGLEIVLPDEEGTILRVGCRTLKCRQ--------------------------- 187 G D VL L VL D G++L LK + Sbjct: 171 GKTSDHVLELISVLYD--GSVLETKPLDLKALEALDALESPSLGQSLQRDIARMTREHRG 228 Query: 188 --------------GYDL-------------ARLIVGSEGTLAIVTEAILKITPMPENVV 220 GYDL +R++ GSEGTLA++TEA L ITP+P+ + Sbjct: 229 EVESRFPKLNRFLTGYDLKNVWNETVDEFNLSRILTGSEGTLAVITEAKLDITPLPKTRM 288 Query: 221 VV----------LAFFPTLRQLVDAVIE-VKSRAIDTLLMEFMDVDSARLAAETLGAAIR 269 +V L P L + V+E V S+ ++ + + + L + GA+I Sbjct: 289 MVNIKYDSFQSALRHAPDLVKAEVTVVETVDSKVLNLAKQDIIWHSVSSLIEDVPGASID 348 Query: 270 PDGHMLLVGVPVNREASTRVLEEMVSIAKAAGAASVYTAK-SMEEAEEKKLLEIRRSLFA 328 + G P EA + LE M+ AA A + + + ++A + +R+ Sbjct: 349 GLNMVEFAGEPDEVEAKVKQLEAMLDTQLAANEAGLLGYQVTSDKASINTIYAMRKKAVG 408 Query: 329 TQALLTQKQFKGRKVMMLMEDIAVPPSKLLDAVERLKELEAKYGFKTVLGGHIGDGNLHP 388 L RK + ED AVPP KL D + + L + + + GH+ G LH Sbjct: 409 ----LLGATKGSRKPIAFAEDTAVPPEKLADFILEFRALLDSHELQYGMFGHVDAGVLHV 464 Query: 389 TISYPVDDEKAKEAALKWYYD-VMRMAIELGGTVSAEHGIGVLKKEALRLELERMGSVKA 447 + + D + E LK D V + ++ GG + EHG GV + + E + Sbjct: 465 RPALDMCDPQ-DERLLKTVSDQVAALTLKYGGLMWGEHGKGVRGEYGPSVFGETL----- 518 Query: 448 LEIMAGIKRVFDPKGILNPGKVVA 471 ++ +K FDP LNPGK+VA Sbjct: 519 FGLLEEVKGYFDPNNKLNPGKLVA 542 Lambda K H 0.319 0.136 0.381 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: 870 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 473 Length of database: 1026 Length adjustment: 39 Effective length of query: 434 Effective length of database: 987 Effective search space: 428358 Effective search space used: 428358 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 (21.7 bits) S2: 54 (25.4 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