Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate Dsui_2542 Dsui_2542 FAD/FMN-dependent dehydrogenase
Query= reanno::Smeli:SMc00832 (479 letters) >FitnessBrowser__PS:Dsui_2542 Length = 468 Score = 185 bits (470), Expect = 3e-51 Identities = 146/477 (30%), Positives = 237/477 (49%), Gaps = 38/477 (7%) Query: 20 EIVADLADLLPEGGLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYG 79 ++ LA ++ +++ E L P+ TD YR LA+V P +T+ VAAV++ C+ G Sbjct: 3 DLQQQLAAIVGPVHVLTGEAELAPYLTDWRGRYRGRALALVKPGSTDEVAAVVRACAAAG 62 Query: 80 IPIVPRGAGTSLSGGAIPQED--AIVVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAV 137 +P+VP+G TSL G A P + +++V LS+++R ID N TV+AG + +A Sbjct: 63 VPMVPQGGNTSLCGAATPDQGGCSVLVNLSRLNRIRQIDAANNAITVEAGCLLAQVQEAA 122 Query: 138 SADGFFYAPDPSSQLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGG 196 +A G + +S+ +C IGGN+ N+GG L+YG T LG+++VL DG + L Sbjct: 123 AAAGRLFPLALASEGSCQIGGNLSTNAGGVQVLRYGNTRELTLGLEVVLPDGRLWNGLTA 182 Query: 197 KALDAPGYDLLGLVCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADIIG 256 D GYDL L G+EG LGI+T A ++L +P R V+ + + + +A ++G Sbjct: 183 LRKDNTGYDLKDLFIGAEGTLGIITAAVLKLFPRP---RAVVTAWLAVADGAAAIA-LLG 238 Query: 257 SGIIP-----VAIEFMDRPAIE-ICEAFAQAGYPLDVEA----LLIVEVEGSEAEMDATL 306 A E + R +++ + + + PL A LL + G+ A++ A L Sbjct: 239 RAQARFDARLTAFELISRQSLDLVLQHIPGSRQPLAAPAPWQVLLELADGGAWADLQADL 298 Query: 307 AGII--EIAR---RHGVMTIRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQ 361 I E+A + GV+ E+Q A +W R++ A I D +VP+S+ Sbjct: 299 EDFIGGEMADGRVQDGVLAQNETQ----ARQLWALRENISEAQKIEGLSIKHDISVPVSR 354 Query: 362 LSHVLRRTGEIVAGY--GLRVANVFHAGDGNMHPLILYNINDPEE------AARAEAAGN 413 + L G +A G+RV HAGDGN+H YN++ + A A Sbjct: 355 IPEFLDLAGTALAAAFPGVRVVAFGHAGDGNLH----YNLSKAQRQDNDTFIAATPQANR 410 Query: 414 DILKLCVEAGGCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKV 470 + L GG ++ EHG+G KR+ ++ L +++ DP+ LMNP K+ Sbjct: 411 IVHDLVARLGGSISAEHGIGQLKREELVRYKDPVGLDLMRCIKSSLDPRGLMNPGKI 467 Lambda K H 0.320 0.138 0.404 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: 590 Number of extensions: 36 Number of successful extensions: 5 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: 479 Length of database: 468 Length adjustment: 33 Effective length of query: 446 Effective length of database: 435 Effective search space: 194010 Effective search space used: 194010 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: 51 (24.3 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