Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate WP_028311103.1 H566_RS0108480 glycolate oxidase subunit GlcE
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >NCBI__GCF_000482785.1:WP_028311103.1 Length = 405 Score = 383 bits (983), Expect = e-111 Identities = 213/409 (52%), Positives = 261/409 (63%), Gaps = 57/409 (13%) Query: 12 LTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHP--------------QGTLLDTRAYSGI 57 + +R + A T L LRGGGSKDFYG P + LLDTR Y+G+ Sbjct: 8 IEGWRARVLDAGRTGRALVLRGGGSKDFYGGVPVADARGAGQSGASAEADLLDTRLYAGV 67 Query: 58 VDYDPPELVITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLS 117 V Y+P EL +TARCGTPLA++EA L E+ QM AFEPPHF GA T+GG AAGLS Sbjct: 68 VAYEPTELYVTARCGTPLAELEALLGEKGQMFAFEPPHFGAGA------TVGGMFAAGLS 121 Query: 118 GPRRQAVGALRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVS 177 GPRR + GALRD+VLG R++DG+G +L+FGGQVMKNVAGYDVSR+++GSLG LG++ EV+ Sbjct: 122 GPRRPSAGALRDYVLGLRLLDGQGRLLNFGGQVMKNVAGYDVSRMLAGSLGVLGIVTEVT 181 Query: 178 LKVLPVPFDDATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAA 237 LK+LP P ++ATLRF L E AAL LN WGGQPLPI+ASAW GVL +RLSG AA+RAA Sbjct: 182 LKLLPRPVEEATLRFELGEDAALAVLNRWGGQPLPISASAWEGGVLTVRLSGQRAAVRAA 241 Query: 238 RARLGGEAVDAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGG----- 292 R +LGGE VD ADA W ALRE + FF P+ AG ALWR+++PTTA G Sbjct: 242 REQLGGERVD--DADAFWAALREQTAPFFRPLAAGEALWRLSLPTTAPAFRAGGAAVAAS 299 Query: 293 -------------------------QLIEWGGGQRWWLGGSDSAADSAIVRAAAKAAGGH 327 QL+EWGGGQRW +++ +RAAA A GGH Sbjct: 300 AAGTASDAGLLPLPPAALQALASAPQLVEWGGGQRWLHAPAEAGP---ALRAAASALGGH 356 Query: 328 ATLFRNGD--KAVGVFTPLSAPVAAIHQRLKATFDPAGIFNPQRMYAGL 374 ATLFR D +A GVFT A + +H LKA FDPA +FN R++ L Sbjct: 357 ATLFRGTDAARAAGVFTHPGAALMRVHAGLKAEFDPARVFNRARLFPEL 405 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: 509 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 374 Length of database: 405 Length adjustment: 30 Effective length of query: 344 Effective length of database: 375 Effective search space: 129000 Effective search space used: 129000 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 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