Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_035391821.1 BA79_RS18270 glycolate oxidase subunit GlcD
Query= reanno::Smeli:SMc00832 (479 letters) >NCBI__GCF_000691145.1:WP_035391821.1 Length = 469 Score = 325 bits (832), Expect = 3e-93 Identities = 173/430 (40%), Positives = 256/430 (59%), Gaps = 2/430 (0%) Query: 44 FETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRGAGTSLSGGAIPQEDAIV 103 + DA +++MP A+V P T E V ++K C+ Y +PIVPRG+GT+L G P + +V Sbjct: 29 YSYDATPNFQQMPDAIVRPHTAEEVQQIVKLCASYKVPIVPRGSGTNLCAGTCPTQGGLV 88 Query: 104 VGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFYAPDPSSQLACTIGGNIGMN 163 + ++M++ L+ID N TATVQ G+ + V G FY PDPSS T+GGNI N Sbjct: 89 ILFTRMNQLLEIDEENLTATVQPGLITQELIHQVEEKGLFYPPDPSSMKISTLGGNINEN 148 Query: 164 SGGAHCLKYGVTTNNLLGVKMVLFDGTVIELGGK-ALDAPGYDLLGLVCGSEGQLGIVTE 222 SGG LKYGVT + +LG+++VL +G +I+ GGK A D GYD+ L GSEG LGIVTE Sbjct: 149 SGGLRGLKYGVTRDYVLGLEVVLPNGDIIKTGGKLAKDVAGYDMTRLFVGSEGTLGIVTE 208 Query: 223 ATVRLIAKPEGARPVLFGFASSESAGSCVADIIGSGIIPVAIEFMDRPAIEICEAFAQAG 282 A ++L+ PE + +L + S E A + V+ II IIP +EFMD+P +E+ E FA G Sbjct: 209 AVLKLLPLPETKQTMLCLYESLEEAATSVSAIIAERIIPATLEFMDQPTLEVVEDFANIG 268 Query: 283 YPLDVEALLIVEVEGSEAEMDATLAGIIEIARRHGVMTIRESQSALEAALIWKGRKSAFG 342 P DV+A+L++E +G+ + + I E+ +HG +++ + S EA+ + R+SA Sbjct: 269 LPTDVQAVLLIEQDGNPEAVSRDIQKIAEVCEQHGATSVKIAHSEEEASALLTARRSALS 328 Query: 343 ATGRIA-DYICMDGTVPLSQLSHVLRRTGEIVAGYGLRVANVFHAGDGNMHPLILYNIND 401 A R++ I D TVP S++++++R +I Y + + HAGDGN+HP + + Sbjct: 329 ALARLSPTTILEDATVPRSEIANMVRAIEDIARKYEVNICTFGHAGDGNLHPTCATDARN 388 Query: 402 PEEAARAEAAGNDILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDP 461 EE R EAA I + V GG +TGEHGVG+ K + + + + A + A DP Sbjct: 389 EEEMKRVEAAFQAIFEKAVALGGTITGEHGVGLMKAPYLELKVKKEGIAAMKAIKQALDP 448 Query: 462 QWLMNPSKVF 471 +MNP KVF Sbjct: 449 AHIMNPDKVF 458 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: 525 Number of extensions: 19 Number of successful extensions: 3 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: 469 Length adjustment: 33 Effective length of query: 446 Effective length of database: 436 Effective search space: 194456 Effective search space used: 194456 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 24 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