Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate 207537 DVU2064 oxidoreductase, 2-nitropropane dioxygenase family
Query= metacyc::HP0773-MONOMER (363 letters) >MicrobesOnline__882:207537 Length = 373 Score = 254 bits (649), Expect = 3e-72 Identities = 147/366 (40%), Positives = 211/366 (57%), Gaps = 28/366 (7%) Query: 8 LKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERIVAKK 67 L+IG + PI QGGMGVGIS LA VA EG +GVI+ G E VAK Sbjct: 6 LQIGDLVARVPIIQGGMGVGISLSRLASAVANEGGIGVIAGAMIG------MKEPDVAKN 59 Query: 68 PFEALNFYSKKALNEIFANARKICGNNPLGANILYAINDYGRVLRDSCEAGANIIITGAG 127 P EA + +AL A + +G NI+ A+ + ++R S E+ A+II +GAG Sbjct: 60 PIEA----NLRALRREIEKAHEAT-KGIVGVNIMVALTTFSEMVRTSIESRADIIFSGAG 114 Query: 128 LPTNMPEFAKDFSD-------VALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPLSG 180 LP ++P D + L+PI+SSA+A ++ K+W R+ +PDAF+VEGP +G Sbjct: 115 LPLDLPRHLHDACEQKKEEFRTKLVPIVSSARAASVIAKKWLSRFDYLPDAFVVEGPKAG 174 Query: 181 GHQGFKYEDCFKEEFRLENLVPKVVEASKEWGN-----IPIIAAGGIWDRKDIDTMLSLG 235 GH GFK E+ LE++VP+V+EA K + + +P+IAAGG++ DI + +G Sbjct: 175 GHLGFKPEEIDDPGHSLEHVVPEVIEAVKPFEDAKGRAVPVIAAGGVYSGDDIRRFIEMG 234 Query: 236 ASGVQMATRFLGTKECDA-KVYADLLPTLKKEDILLIKSPVGYPARAINTGVIKRIEEGN 294 A+GVQM TRF+ T ECDA + + ++ED+ +IKSPVG P RAI G I+ + EG Sbjct: 235 AAGVQMGTRFVATHECDADERFKQAYVAAREEDVTIIKSPVGMPGRAIGNGFIEAMREGA 294 Query: 295 APKIACVSNCVAPCNRGEEAKKVGYCIADGLGRSYLGNREEGLYFTGANGYRVDKIISVH 354 CV C++ C E ++ YCIA L + GN E+G F+G+N +R+D I+SV Sbjct: 295 KKPFKCVFKCISTC----EQEQTPYCIAAALINAMKGNLEKGFAFSGSNVFRIDSILSVR 350 Query: 355 ELIKEL 360 +LI L Sbjct: 351 DLIGSL 356 Lambda K H 0.319 0.139 0.418 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: 385 Number of extensions: 25 Number of successful extensions: 6 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: 363 Length of database: 373 Length adjustment: 30 Effective length of query: 333 Effective length of database: 343 Effective search space: 114219 Effective search space used: 114219 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 (21.7 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