Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate WP_011764734.1 AZO_RS05045 glycolate oxidase subunit GlcE
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >NCBI__GCF_000061505.1:WP_011764734.1 Length = 353 Score = 415 bits (1067), Expect = e-121 Identities = 215/363 (59%), Positives = 264/363 (72%), Gaps = 14/363 (3%) Query: 12 LTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELVITARC 71 ++A+ D IR A TPL+LRGGG+K FYG+ +G +LD G+V Y+P ELV+T R Sbjct: 5 VSAWADRIRAAAAADTPLQLRGGGTKAFYGRSGEGEVLDLTDNRGVVSYEPTELVVTVRG 64 Query: 72 GTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALRDFV 131 GTPLA++EA LA Q LAFEPP F A T+GG VAAGLSGPRR + GA+RDFV Sbjct: 65 GTPLAELEALLARHDQFLAFEPPAFGPAA------TVGGCVAAGLSGPRRASAGAVRDFV 118 Query: 132 LGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDATLR 191 LG R++DGRG+ LSFGGQVMKNVAGYDVSRL++GSLGTLG++LEVSLKVLP P +ATLR Sbjct: 119 LGARLLDGRGEALSFGGQVMKNVAGYDVSRLLAGSLGTLGVLLEVSLKVLPRPAAEATLR 178 Query: 192 FALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARARLGGEAVDAAQA 251 F DEA+A+ RLNDWGGQPLP++AS WHDGVL +RLSGA+AA+ AA+ARLGGE +D A A Sbjct: 179 FECDEASAIQRLNDWGGQPLPLSASTWHDGVLTVRLSGASAAVAAAQARLGGERLDEALA 238 Query: 252 DALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGGQRWWLGGSDSA 311 A W ++REH+ AP A R LWR+++P++AAPL L GGQLIEWGG RW + Sbjct: 239 TAFWTSIREHT----APWFAARPLWRLSLPSSAAPLRLAGGQLIEWGGALRW----LHTD 290 Query: 312 ADSAIVRAAAKAAGGHATLFRNGDKAVGVFTPLSAPVAAIHQRLKATFDPAGIFNPQRMY 371 + VR GG A LF G+++ VF PL P+ IH+RLKA FDPAGIFN R+Y Sbjct: 291 LPATAVRERVAQLGGTAALFAGGNRSGEVFHPLPEPLLRIHRRLKAAFDPAGIFNRGRLY 350 Query: 372 AGL 374 GL Sbjct: 351 QGL 353 Lambda K H 0.321 0.136 0.414 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: 439 Number of extensions: 22 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: 374 Length of database: 353 Length adjustment: 29 Effective length of query: 345 Effective length of database: 324 Effective search space: 111780 Effective search space used: 111780 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: 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