Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate 3609512 Dshi_2896 FAD linked oxidase domain protein (RefSeq)
Query= BRENDA::O29853 (443 letters) >FitnessBrowser__Dino:3609512 Length = 480 Score = 202 bits (514), Expect = 2e-56 Identities = 138/438 (31%), Positives = 229/438 (52%), Gaps = 31/438 (7%) Query: 18 DAYRFDETPPLVAPRAAENFVVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVP 77 DA + PPL A V PS++EEV+A+LK + + +PV RG GT L+GGA+P Sbjct: 43 DALTAYKCPPLAA---------VLPSSTEEVAAVLKICHAEGVPVVPRGSGTSLAGGALP 93 Query: 78 TEEGIVLSTEKMTE-LEVDADNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVG 135 T + ++L ++ + LE D DNR+ +G T + A + P P ++ A + Sbjct: 94 TADCVILGVARLNKVLETDYDNRIIRVQSGRTNLSVSGAVEEEDFFYAPDPSSQLACAIA 153 Query: 136 GMIATNAGGVRALKYGTMRNYVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGT 195 G IA N+GG LKYG N +L + V+ DG ++ +GG + ++ G LL ++ GSEG Sbjct: 154 GNIAMNSGGAHCLKYGVTTNNLLGVTMVMMDGTVVTIGGAHL-DAGGLDLLGVICGSEGQ 212 Query: 196 LAVITKATIRLFPQMRDMTVLAIPFPTMEDAMNCVVEVARK-MLPMALEFMEKRAVEIGE 254 L V+T+AT+R+ + + I F E A CV ++ + +LP+A+EFM+K +E E Sbjct: 213 LGVVTEATLRILRKPEGARPVLIAFDENEVAGACVADIIKAGVLPVAIEFMDKLCIETCE 272 Query: 255 KVSGERWVSREGEAHLLMVFESFDEAEEAAK------IAQSLGAIDVYAATTKKDQDRLL 308 + + E LL+V EAE A+ IA+ +++ + + ++ ++ Sbjct: 273 NFAKAGYPECEA---LLIVEVEGSEAEIDAQLGVILDIARKHNPVELRQSQSAEESAKIW 329 Query: 309 KVRGMIYEGL-RKEVIEVLDACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQH 367 R + + + LD +P +++ RR E+++EYG+++ HAGDGN+ H Sbjct: 330 LGRKSAFGAIGQLNDYMCLDGTIPVSELPYVLRRIGEMSKEYGLQVGNVFHAGDGNM--H 387 Query: 368 PLVY-----EGWEKSYFEFRKSLLSLAVSLGGVISGEHGIGAVKLSELEELFP-EQFELM 421 PL+ +G + F +L L V +GG ++GEHG+G K + F E+ Sbjct: 388 PLILFDANKDGDLELCEAFGAEILKLCVEVGGCLTGEHGVGIEKRDLMGAQFTGADMEMQ 447 Query: 422 RQIKLLFDPKNILNPGKV 439 ++K +FDP +LNP KV Sbjct: 448 LRVKDVFDPAWLLNPAKV 465 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: 488 Number of extensions: 23 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: 480 Length adjustment: 33 Effective length of query: 410 Effective length of database: 447 Effective search space: 183270 Effective search space used: 183270 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 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