Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate 206254 DVU0827 glycolate oxidase, subunit GlcD, putative
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >MicrobesOnline__882:206254 Length = 471 Score = 101 bits (252), Expect = 4e-26 Identities = 120/412 (29%), Positives = 174/412 (42%), Gaps = 65/412 (15%) Query: 17 DAIRHATGTRTPLRLRGGGSKDFYGQHPQ--GTLLDTRAYSGIVDYDPPELVITARCGTP 74 + +R A R P+ R + G PQ G +L T + I+D D + V + G Sbjct: 68 ELLRWADAERLPVYPRARATNVVGGCVPQRPGIVLSTLRMARIIDIDEHDFVAVVQPGVI 127 Query: 75 LAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALRDFVLGT 134 A ++ A+ R F PP ++ ++++IGG VA G R G RD+VLG Sbjct: 128 TADLQRAVEARG---LFYPPDPAS----QNISSIGGNVATCAGGMRAVRYGVTRDYVLGL 180 Query: 135 RVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDATLRFAL 194 R + G+VL+ G + KNV G D+ RL+ GS GTLG + EV+LK+LP+P A+L Sbjct: 181 RAVLPGGEVLATGSRCHKNVVGLDLVRLLVGSEGTLGCLTEVTLKLLPLPEATASLLAGF 240 Query: 195 -DEAAALDRL-NDWGGQPLPIA-----------ASAWHD--------GVLHLRLSGAAAA 233 D AA+D + N + LP+A A+ +D L RL G+ AA Sbjct: 241 SDLGAAMDAVRNVFAAGILPVALEFMGPEVLDCAALLNDVPWPKTVRAALLFRLDGSRAA 300 Query: 234 LRAARARLGGEAVDAA-----------QADALWRALREHSHAFFAPVQAGRALWRIAVPT 282 L RL DAA + + LW R + A F V+ + + VP Sbjct: 301 LPLEVDRLAAAVRDAAPVWSAVGVGRDEEEPLWTIRRSINPASFL-VKPDKMSDDVTVPR 359 Query: 283 TAAPLALPGGQLIEWGGGQRWWLGGS--------DSAADSAIV--RAAAKAAGGHATLF- 331 AL G + I G + D+++ R A AA G T Sbjct: 360 GRLREALEGIRAIAEARSLTILTFGHVGDGNIHVNIMHDASVTEEREHALAAKGEVTDLI 419 Query: 332 ------RNGDKAVG------VFTPLSAPVAAIHQRLKATFDPAGIFNPQRMY 371 +G+ VG V LS + ++KA FDP GI NP + Y Sbjct: 420 LSLGGTLSGEHGVGLTKAPYVHRQLSKLERGLMAQVKAAFDPHGIMNPGKAY 471 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: 380 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 374 Length of database: 471 Length adjustment: 32 Effective length of query: 342 Effective length of database: 439 Effective search space: 150138 Effective search space used: 150138 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: 50 (23.9 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