Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate RR42_RS29880 RR42_RS29880 glycolate oxidase
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >FitnessBrowser__Cup4G11:RR42_RS29880 Length = 357 Score = 358 bits (919), Expect = e-103 Identities = 194/358 (54%), Positives = 240/358 (67%), Gaps = 13/358 (3%) Query: 17 DAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELVITARCGTPLA 76 + + HA T+T L + GGG+K FYG+ P G D R SGI Y+P ELV+TAR GTPL Sbjct: 13 ETVLHARKTKTSLNIVGGGTKCFYGEEPSGEPCDVRRLSGICSYEPSELVVTARAGTPLE 72 Query: 77 QIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALRDFVLGTRV 136 ++EA LAE Q LAFEPP F+ G+ T+GGAVAAGLSGP R VG++RDFVLG + Sbjct: 73 ELEAVLAEHNQYLAFEPPRFAKGS------TVGGAVAAGLSGPARVGVGSIRDFVLGATM 126 Query: 137 MDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDATLRFALDE 196 ++G+G++L+FGGQVMKNVAGYDVSRL++GS+G LG+I EVSLKVLP+ TL DE Sbjct: 127 INGKGELLTFGGQVMKNVAGYDVSRLLAGSMGILGVICEVSLKVLPIHSSRITLFIERDE 186 Query: 197 AAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARARLGGEAVDAAQADALWR 256 A AL LN Q LP+ ASAWHDG L LRLSGAA+A+ AR RLGG ++ +A + W Sbjct: 187 AGALSLLNGLTRQALPVNASAWHDGKLFLRLSGAASAVTEARKRLGGTELEPDEALSWWD 246 Query: 257 ALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGGQRWWLGGSDSAADSAI 316 A+R+H H FF+ Q+ LWR++VP + P L QLIEWGG R WL D D Sbjct: 247 AVRDHRHDFFS--QSDAPLWRVSVPAVSQPF-LAANQLIEWGGALR-WLYTDDPIED--- 299 Query: 317 VRAAAKAAGGHATLFRNGDKAVGVFTPLSAPVAAIHQRLKATFDPAGIFNPQRMYAGL 374 VR A + GGHATLFR+ GVFTP S + IH+ LK FDP GIFN R+Y GL Sbjct: 300 VREMASSLGGHATLFRDPHHRSGVFTPPSDALFEIHRNLKQAFDPDGIFNVGRLYPGL 357 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: 373 Number of extensions: 17 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: 357 Length adjustment: 30 Effective length of query: 344 Effective length of database: 327 Effective search space: 112488 Effective search space used: 112488 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 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