Align D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate WP_086511791.1 BZY95_RS20760 glycolate oxidase subunit GlcE
Query= reanno::psRCH2:GFF3771 (353 letters) >NCBI__GCF_002151265.1:WP_086511791.1 Length = 363 Score = 421 bits (1081), Expect = e-122 Identities = 217/352 (61%), Positives = 261/352 (74%), Gaps = 6/352 (1%) Query: 6 NDASAQLLDQVNQALAANTPLRIQGSGSKSFLGLQADGVLLDTREHRGIVSYDPTELVVT 65 +DA A L +++ QA A TPLRI G ++ F G + +G L T EHRGI YDP ELVV+ Sbjct: 10 HDAGADLAERIRQASAEGTPLRIIGGDTRYFYGREVEGSELSTHEHRGISFYDPVELVVS 69 Query: 66 VRAGTPLTELETALDEAGQMLPCEPPHFGEGATVGGMIAAGLSGPRRPWSGSVRDFVLGS 125 VRAGTPL ELE AL E GQMLP EPP +G +TVGGM+A GLSGPRRPW+GSVRDFVLG+ Sbjct: 70 VRAGTPLAELEAALAEQGQMLPFEPPRYGIASTVGGMVATGLSGPRRPWAGSVRDFVLGT 129 Query: 126 RVITGQGKHLRFGGEVMKNVAGYDLSRLMAGSFGCLGVLTEVSLKVLPKPRLCTSLRLEI 185 RVI +G RFGGEVMKNVAGYDLSRLM G+ G LG++TEVS KVLP P SL LE+ Sbjct: 130 RVINHEGIEQRFGGEVMKNVAGYDLSRLMVGAQGGLGLITEVSFKVLPIPGATQSLHLEL 189 Query: 186 DLERALLKLAEWGQQPIPISAASHDGQALHLRLEGGEGSVGAARERIGGEDLDPGYWNDL 245 L+ A L+LAEWG++P+PISAA+ ALHLRLEGG SV A R RIGG+DLD G+W L Sbjct: 190 SLDEARLRLAEWGREPLPISAAAWLDGALHLRLEGGPSSVAATRARIGGDDLDNGFWTAL 249 Query: 246 REQRLAFFADPR-PLWRLSLPNNTPALGLP--GDQLV--DWAGAQRWLKSDADAVTIRGI 300 R+QRL FF++ R PLWRLSLP+ TPAL LP ++L+ DWAGAQRWL+++ DA T+R Sbjct: 250 RDQRLPFFSEGRAPLWRLSLPHRTPALELPDVDERLMIHDWAGAQRWLRAELDAETLRRT 309 Query: 301 AIEVGGHATCF-TAGATTNPFQPLAAPLLRYHRQLKAALDPQGIFNPGRMYS 351 GGHATC+ A PF PL L++YHR LKA LDP+GIFNPGR+Y+ Sbjct: 310 CQAAGGHATCYGPRPADVEPFTPLPEVLMKYHRNLKAQLDPKGIFNPGRLYA 361 Lambda K H 0.319 0.137 0.417 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: 482 Number of extensions: 26 Number of successful extensions: 4 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: 353 Length of database: 363 Length adjustment: 29 Effective length of query: 324 Effective length of database: 334 Effective search space: 108216 Effective search space used: 108216 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 (21.7 bits) S2: 49 (23.5 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