Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate AZOBR_RS29745 AZOBR_RS29745 2-hydroxyacid dehydrogenase
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__azobra:AZOBR_RS29745 Length = 467 Score = 183 bits (464), Expect = 1e-50 Identities = 138/466 (29%), Positives = 226/466 (48%), Gaps = 18/466 (3%) Query: 21 IVADLADLLPEGGLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGI 80 ++A + ++ + GLI+D ++PF + AVVLP++TE +AAV++ C+ Sbjct: 1 VLAPIRAIVGDRGLITDPDTMQPFMESWRDGWVGRSPAVVLPDSTEALAAVVRICAETRT 60 Query: 81 PIVPRGAGTSLSGGAIPQEDA--IVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVS 138 PIVP+G T L+G + P D IV+ ++++R +ID+ N T TV+AG NI +A Sbjct: 61 PIVPQGGNTGLTGASQPHADGTEIVLSTNRLNRIREIDIDNDTMTVEAGCILANIQNAAR 120 Query: 139 ADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGGK 197 G + +++ +C IGGNI N+GG ++YG N + G+++VL DG + + L G Sbjct: 121 DIGRLFPMSLAAEGSCQIGGNIATNAGGVQVVRYGNMRNLVAGLEVVLPDGRIWDGLRGL 180 Query: 198 ALDAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADIIG- 256 D GYD+ + GSEG LGIVT A ++L P L ++ A + G Sbjct: 181 RKDNAGYDMKQIFIGSEGTLGIVTAAVLKLSPLPRATATALVAVSAPSDAVDLLTRAKGV 240 Query: 257 SGIIPVAIEFMDRPAIEICEAFA-------QAGYPLDVEALLIVEVEGSEAEMDATLAGI 309 +G + E + R I++ + YP V + + + +G M+ L GI Sbjct: 241 AGDRIITFELIQRDCIDVARRHVPDVPDPLRDRYPWYV-LVELADQDGGNRLME-MLEGI 298 Query: 310 IEIARRHG-VMTIRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQLSHVLRR 368 +E G V+ + S +A +W+ R+ R D +VP+S+++ L R Sbjct: 299 LEAGMEAGEVLDGVVAASKAQADSLWRIREGIPEGQKREGVSFKHDVSVPISRVARFLDR 358 Query: 369 TGEIVAGY--GLRVANVFHAGDGNMH--PLILYNINDPEEAARAEAAGNDILKLCVEAGG 424 + G+R H GDGN+H P+ + E A+ + + VE GG Sbjct: 359 ANAALERECPGIRPFAFGHLGDGNIHFNPIQAEGGDPAEWKAKLATVNAIVHDIVVELGG 418 Query: 425 CLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKV 470 ++ EHG+G + D M S +L + AFDP +MNP K+ Sbjct: 419 SISAEHGIGRLRIDEMPRYKSAVELDMMATLKRAFDPHNIMNPGKI 464 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: 612 Number of extensions: 31 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: 1 Length of query: 479 Length of database: 467 Length adjustment: 33 Effective length of query: 446 Effective length of database: 434 Effective search space: 193564 Effective search space used: 193564 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