Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate 8500002 DvMF_0766 2-nitropropane dioxygenase NPD (RefSeq)
Query= metacyc::HP0773-MONOMER (363 letters) >FitnessBrowser__Miya:8500002 Length = 373 Score = 262 bits (670), Expect = 1e-74 Identities = 155/372 (41%), Positives = 214/372 (57%), Gaps = 36/372 (9%) Query: 8 LKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERIVAKK 67 L IG + PI QGGMGVGIS LA VA EG +GVI+A G E VAK Sbjct: 6 LNIGDLVARIPIVQGGMGVGISLSRLASAVANEGGIGVIAAAMIG------MKEPDVAKN 59 Query: 68 PFEALNFYSKKALNEIFANARKICGNNPLGANILYAINDYGRVLRDSCEAGANIIITGAG 127 P EA + +AL AR++ +G NI+ A+ +G ++R S E A+II +GAG Sbjct: 60 PIEA----NVRALRRELQKAREMT-QGIVGVNIMVALTTFGEMVRTSIEERADIIFSGAG 114 Query: 128 LPTNMPEFAKDFSD-------VALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPLSG 180 LP ++P ++ D L+PI+SSA+A ++ K+W R+ +PDAF+VEGP +G Sbjct: 115 LPLDLPRHLREACDQKKEEFRTKLVPIVSSARAASVIAKKWITRFDYVPDAFVVEGPKAG 174 Query: 181 GHQGFKYEDCFKEEFRLENLVPKVVEASKEWGN-----IPIIAAGGIWDRKDIDTMLSLG 235 GH GFK E+ LE ++P+VVEA K + + IP+IAAGG++ +DI + LG Sbjct: 175 GHLGFKAEEIDDPNHSLEAVIPQVVEAVKPFEDQKGCRIPVIAAGGVYTGEDITRFMELG 234 Query: 236 ASGVQMATRFLGTKECDA-----KVYADLLPTLKKEDILLIKSPVGYPARAINTGVIKRI 290 A+GVQM TRF+ T ECDA + Y D ++D+ +IKSPVG P RAI I + Sbjct: 235 AAGVQMGTRFVATHECDADDRFKQAYVD----ATEQDVTIIKSPVGMPGRAIGNSFIDSM 290 Query: 291 EEGNAPKIACVSNCVAPCNRGEEAKKVGYCIADGLGRSYLGNREEGLYFTGANGYRVDKI 350 EG CV C++ C E ++ YCIA L + GN E+G F+GAN +RVD+I Sbjct: 291 REGAKKPFKCVFKCISTC----EQEQTPYCIAAALINAMKGNLEKGFAFSGANVFRVDRI 346 Query: 351 ISVHELIKELTE 362 SVHEL+ L + Sbjct: 347 QSVHELVSSLQQ 358 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: 383 Number of extensions: 26 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