Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS03515 BPHYT_RS03515 D-lactate dehydrogenase
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__BFirm:BPHYT_RS03515 Length = 471 Score = 223 bits (569), Expect = 8e-63 Identities = 135/422 (31%), Positives = 215/422 (50%), Gaps = 8/422 (1%) Query: 54 RMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIVVGLSKMSRTL 113 ++P AVV TTE V ++K C +Y +PI+P G G+SL G + + + + LS+M+R L Sbjct: 50 QLPDAVVFARTTEDVQTIVKLCGQYNVPIIPYGNGSSLEGHLLAVQGGVSIDLSEMNRVL 109 Query: 114 DIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYG 173 I+ + T TV+ G++ +++A+ G F+ DP + +IGG + G + ++YG Sbjct: 110 SINAEDLTVTVEPGISRKQLNEALRDTGLFFPIDPGAD--ASIGGMSATRASGTNAVRYG 167 Query: 174 VTTNNLLGVKMVLFDGTVIELGGKAL-DAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPE 232 N+LG+ +VL DG VI+ G +A + GYDL + GSEG LG++TE TVRL +PE Sbjct: 168 TMRENVLGLTVVLADGRVIKTGTRARKSSAGYDLTRMFVGSEGTLGVITEITVRLYPQPE 227 Query: 233 GARPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAGYPLDVEALLI 292 + F S +A V + I G+ +EF+D AI + L L Sbjct: 228 AVSAAVCAFPSMGAAVRAVIETIQMGVPIARVEFVDSLAIRSINR--HSNLTLREAPTLF 285 Query: 293 VEVEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFGATGRIAD--- 349 E G+EA + + EIA ++ + + + +W R +A+ A ++ Sbjct: 286 FEFHGTEAGVKEQAELVQEIAAQNAGEGFEWATRPEDRSRLWNARHNAYFAMLQLKPGCR 345 Query: 350 YICMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNINDPEEAARAE 409 + D VP+S+L+ + T + + L V H GDGN H IL + N PEE AE Sbjct: 346 AVTTDVCVPISRLAECVEETEQDLQASPLPCPIVGHVGDGNFHVAILIDPNKPEELVEAE 405 Query: 410 AAGNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSK 469 + I++ + G TGEHGVG+ K +L ++ + + + A DP LMNP K Sbjct: 406 RLNHRIVQRALRMDGTCTGEHGVGLHKMGFLLEEHGEVAVDTMRSIKHALDPHNLMNPGK 465 Query: 470 VF 471 +F Sbjct: 466 IF 467 Lambda K H 0.320 0.138 0.404 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: 537 Number of extensions: 17 Number of successful extensions: 4 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: 479 Length of database: 471 Length adjustment: 33 Effective length of query: 446 Effective length of database: 438 Effective search space: 195348 Effective search space used: 195348 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: 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