Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate WP_027720221.1 H589_RS0100550 nitronate monooxygenase
Query= metacyc::HP0773-MONOMER (363 letters) >NCBI__GCF_000425265.1:WP_027720221.1 Length = 359 Score = 252 bits (643), Expect = 1e-71 Identities = 141/362 (38%), Positives = 208/362 (57%), Gaps = 21/362 (5%) Query: 5 LKPLKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERIV 64 L LKIG K P+ QGGMGVGIS LA VAKEG +GVI+A G + Sbjct: 3 LPQLKIGDLVAKVPVIQGGMGVGISLSGLASAVAKEGGIGVIAAAMIGLTSKNGGKDH-- 60 Query: 65 AKKPFEALNFYSKKALNEIFANARKICGNNPLGANILYAINDYGRVLRDSCEAGANIIIT 124 AK +AL +KA K + LG NI+ A++++ ++ S + GA++I + Sbjct: 61 AKAHIDALTEEIRKA---------KEMTSGILGVNIMVALSNFADMVSTSVKEGADVIFS 111 Query: 125 GAGLPTNMPEFAKDFSDVALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPLSGGHQG 184 GAGLP ++P++ + + L+PI+SS +A I+CK+W R+ IPDAF+VEGP +GGH G Sbjct: 112 GAGLPLDLPKYVTEGAKTKLVPIVSSGRAASIICKKWISRFDYIPDAFVVEGPKAGGHLG 171 Query: 185 FKYEDCFKEEFRLENLVPKVVEASKEW-----GNIPIIAAGGIWDRKDIDTMLSLGASGV 239 FK E F LE ++P+V++A K + NIP+IAAGG++ +DI + +GA+GV Sbjct: 172 FKREQLDDPLFALEKILPEVIKAVKPFEEKTGRNIPVIAAGGVYSGEDICKYIEMGAAGV 231 Query: 240 QMATRFLGTKECDAK-VYADLLPTLKKEDILLIKSPVGYPARAINTGVIKRIEEGNAPKI 298 QM TRF+ T ECDA + ++D+ +I+SPVG P RA+ ++ + +G Sbjct: 232 QMGTRFVATHECDANDEFKQAYVNSTEDDMTIIQSPVGLPGRAVKNAFLQAVTDGQKAPF 291 Query: 299 ACVSNCVAPCNRGEEAKKVGYCIADGLGRSYLGNREEGLYFTGANGYRVDKIISVHELIK 358 C +C+ C + +K YCIA L + G + G F G+N +R DKIISV +L Sbjct: 292 KCPFHCIKSC----KVEKSPYCIASALINAQRGKLKNGFAFAGSNAWRTDKIISVKQLFT 347 Query: 359 EL 360 +L Sbjct: 348 DL 349 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: 382 Number of extensions: 24 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: 363 Length of database: 359 Length adjustment: 29 Effective length of query: 334 Effective length of database: 330 Effective search space: 110220 Effective search space used: 110220 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 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