Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_011385361.1 AMB_RS15030 FAD-binding protein
Query= reanno::Smeli:SMc00832 (479 letters) >NCBI__GCF_000009985.1:WP_011385361.1 Length = 457 Score = 211 bits (538), Expect = 3e-59 Identities = 139/419 (33%), Positives = 208/419 (49%), Gaps = 9/419 (2%) Query: 56 PLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIVVGLSKMSRTLDI 115 P AVV ++TE VA +K C+ +G P++ G GTSL G + + + +S M+R L++ Sbjct: 41 PEAVVFAQSTEEVAETVKACAAHGTPVIAFGTGTSLEGHVAALKGGVCIDVSGMNRVLEV 100 Query: 116 DLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVT 175 + TVQ GVT +++ + G F+ DP + ++GG + G + ++YG Sbjct: 101 RAEDLDVTVQPGVTRKQLNEYLRDTGLFFPIDPGAD--ASLGGMAATRASGTNAVRYGTM 158 Query: 176 TNNLLGVKMVLFDGTVIELGGKA-LDAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGA 234 N+L +++VL DG VI G+A + GYDL L GSEG LGI+TE T+RL PE Sbjct: 159 RENVLSLQVVLPDGRVIRTAGRARKSSAGYDLTRLFVGSEGTLGIITELTLRLQGIPEAI 218 Query: 235 RPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAGYPLDVEALLIVE 294 + F S E+A + V I SG+ IEF+D+ I +++ + L E Sbjct: 219 SAAVCPFPSIEAAVNTVILTIQSGVPVARIEFLDKVMIGAVNRYSKTDH--REAPTLFFE 276 Query: 295 VEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFGATGRIADYI--- 351 GS A + + IA G + + A E +W R +A+ A + Sbjct: 277 FHGSPASVQEQAEKVEAIATEFGAEGFQWATGAEERTKLWAARHNAYYAGVGLRPGCRAW 336 Query: 352 CMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNINDPEEAARAEAA 411 D VP+S+L+ L T E + L A V H GDGN H ++L + PEEAA AE Sbjct: 337 TTDACVPISRLAECLLETEEDLKTTPLISAIVGHVGDGNFHVMLLVDPGKPEEAAEAERI 396 Query: 412 GNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKV 470 + I++ + G TGEHGVG K + +Y A L A + A DP +MNP K+ Sbjct: 397 NHRIVRRALAMDGTCTGEHGVGHGKMAFLEEEYGEA-LDVMRAVKRAIDPAGIMNPGKI 454 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: 557 Number of extensions: 26 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: 479 Length of database: 457 Length adjustment: 33 Effective length of query: 446 Effective length of database: 424 Effective search space: 189104 Effective search space used: 189104 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