Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate AZOBR_RS05770 AZOBR_RS05770 2-hydroxyacid dehydrogenase
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__azobra:AZOBR_RS05770 Length = 462 Score = 182 bits (462), Expect = 2e-50 Identities = 145/458 (31%), Positives = 220/458 (48%), Gaps = 22/458 (4%) Query: 33 GLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLS 92 GL++ + P+ ++ ++ AVV P +TE VAAV+ C+ GIP+VP+G TSL Sbjct: 9 GLLTAPEDMAPYLSEWRGRFKGNSPAVVRPASTEEVAAVVTICAEAGIPVVPQGGNTSLV 68 Query: 93 GGAIPQEDA--IVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSS 150 GG+IP E+ IV+ LS+M++ ID N T TV+AGV +A + Sbjct: 69 GGSIPYEEGREIVISLSRMNKIRGIDTLNYTMTVEAGVVLKTAQEAAKDKDRLLPMSLGA 128 Query: 151 QLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGGKALDAPGYDLLGL 209 + C IGG I N+GG + L+YG + +LG+++VL DG V L + GYDL L Sbjct: 129 EGTCQIGGLISTNAGGINVLRYGNMRDLVLGLEVVLADGRVWNGLRSLRKNNTGYDLKHL 188 Query: 210 VCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADI-IGSGIIPVAIEFMD 268 G+EG LGIVT A ++L +P A S +A +A + SG A E M Sbjct: 189 FIGAEGTLGIVTAAVLKLYPRPRQAETAFIAVPSPAAAIELLARLREASGDAVAAFELMS 248 Query: 269 RPAIEIC-EAFAQAGYPLDVEALLIVEVE-----GSEAEMDATLAGIIEIARRHGVMTIR 322 R +E + A PL + V E S+A + A + E Sbjct: 249 RRCLEFALKHVAGTIDPLSEPSPWYVLTELTAGTQSDAFRETVEAALGEAFEAELATDAT 308 Query: 323 ESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQLSHVLRR--TGEIVAGYGLRV 380 +QS +A +W R++ A I D +VP+S+++ + R + A G+R Sbjct: 309 IAQSETQANQLWFIREAIVEAQKFEGGSIKNDVSVPVSRVAEFIERAEAAVVAACPGIRP 368 Query: 381 ANVFHAGDGNMHPLILYNINDPEEA------ARAEAAGNDILKLCVEAGGCLTGEHGVGI 434 H GDGN+H +N++ PE A AR + + + ++ G ++ EHGVG Sbjct: 369 TPFGHVGDGNIH----FNLSQPEGADTAAYLARWDEICHVVNEVIFALDGSISAEHGVGR 424 Query: 435 EKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKVFP 472 K+D M S + A +AA DP+ L+NP K+ P Sbjct: 425 FKKDEMPVIKSPVEFDLLRAMKAALDPKGLLNPGKMLP 462 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: 628 Number of extensions: 32 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: 462 Length adjustment: 33 Effective length of query: 446 Effective length of database: 429 Effective search space: 191334 Effective search space used: 191334 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