Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Ac3H11_2934 D-2-hydroxyglutarate dehydrogenase
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2934 Length = 474 Score = 181 bits (460), Expect = 4e-50 Identities = 145/459 (31%), Positives = 225/459 (49%), Gaps = 35/459 (7%) Query: 38 ERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIP 97 E L +E D R LAVV P T+ VAAV+K C+ G IVP+G T L+ G+ P Sbjct: 20 EGDLTAWEQDWRRRVRGKALAVVRPANTQEVAAVVKACAAVGTAIVPQGGNTGLAVGSTP 79 Query: 98 QEDA--IVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACT 155 + IV+ L++M+ +D N T TV+AG N+ D G + +++ +CT Sbjct: 80 DDSGTQIVLSLTRMNAVRSVDTDNLTMTVEAGCILQNLQDVAQNAGVLFPLSLAAEGSCT 139 Query: 156 IGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGGKALDAPGYDLLGLVCGSE 214 IGGN+G N+GG ++YG + LG+++V G V + L G D GYDL L GSE Sbjct: 140 IGGNLGTNAGGTQVVRYGNARDLCLGLEVVTAQGEVWDGLKGLRKDNTGYDLRDLFIGSE 199 Query: 215 GQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADI------IGSGIIPVAIEFMD 268 G LGI+T AT++L +P L +A++ S VA + +G+G+ E M Sbjct: 200 GTLGIITAATMKLYPQPAAN---LTAWAAAPSMEHAVALLGLAHKQLGAGL--TGFEVMG 254 Query: 269 RPAIEIC-EAFAQAGYPL--DVEALLIVEVEGSEAEMD----ATLAGIIEIARRHGVMT- 320 + A+ + + Q P D A V +E S++E + A ++E A G +T Sbjct: 255 QFALSLVGKHMPQLRVPFLGDDNAPWCVLLENSDSESEEHARARFESLLETAFEMGCVTD 314 Query: 321 IRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQLSHVLRRTGEIVAGY--GL 378 +++ +A +W R+S A I D ++ +S++ + T ++ G+ Sbjct: 315 AVVAENLTQAHQLWHIRESIPLAQAEEGLNIKHDISIQISRIPAFVAHTDAVLQREIPGV 374 Query: 379 RVANVFHAGDGNMHPLILYNI-----NDPEEAARAEAA--GNDILKLCVEAGGCLTGEHG 431 R+ N H GDGN+H YN+ DP+ R + A + + + E GG + EHG Sbjct: 375 RLVNFGHLGDGNLH----YNVQAPAAGDPKAFLREQEARVNHLVYEAVAEFGGSFSAEHG 430 Query: 432 VGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKV 470 +G K D + S LG A + A DPQ +MNP +V Sbjct: 431 IGELKADKLAKYQSPVALGMMRAIKQALDPQGVMNPGRV 469 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: 517 Number of extensions: 20 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: 474 Length adjustment: 33 Effective length of query: 446 Effective length of database: 441 Effective search space: 196686 Effective search space used: 196686 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