Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate Dsui_1637 Dsui_1637 2-nitropropane dioxygenase-like enzyme
Query= metacyc::HP0773-MONOMER (363 letters) >FitnessBrowser__PS:Dsui_1637 Length = 387 Score = 179 bits (454), Expect = 1e-49 Identities = 128/377 (33%), Positives = 197/377 (52%), Gaps = 23/377 (6%) Query: 7 PLKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERIVAK 66 PLKI T+ PI QGGMGVGIS LAG VA +G I++V + E ++ Sbjct: 8 PLKIKGKTL-VPIVQGGMGVGISAHRLAGTVASLNGVGTIASVDLRRHHPDLMAETGRSR 66 Query: 67 KPFEALNFYSKKALNEIFANARKIC-GNNPLGANILYAINDYGRVLRDSCEAGANIIITG 125 EA+ + AL+ A+ I G + N++ A+ Y +R SC++GA I+ G Sbjct: 67 NR-EAIEKANLIALDREIKMAQDIAQGRGVIAVNVMRAVTQYQDYVRQSCQSGAEAIVMG 125 Query: 126 AGLPTNMPEFAKDFSDVALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGP-LSGGHQG 184 AGLP ++PE + + DVAL+PI+S + + +L K+W R R+PDA ++E P +GGH G Sbjct: 126 AGLPLDLPELTEGYPDVALVPILSDVRGIVLLLKKWM-RKNRLPDAIVIEHPRYAGGHLG 184 Query: 185 -FKYEDCFKEEFRLENLVPKVVEASKEWG----NIPIIAAGGIWDRKDIDTMLSLGASGV 239 K ED F E ++P V+EA +E G IP+I AGGI + + ++ +GA+ V Sbjct: 185 AAKKEDVNDPRFNFEVVIPGVLEAFEEMGIASEKIPLIPAGGINSHERVRELIDMGAAAV 244 Query: 240 QMATRFLGTKECDAKV-YADLLPTLKKEDILLIKSPVGYPARAINTGVIKRI---EE--- 292 Q+ + F +E DA + + +L K +D++ S G PARA+ T +++ EE Sbjct: 245 QLGSAFAVAEEGDADIEFKKVLAGAKDKDVVDFMSCAGLPARAVKTPWLEKYLNREEKLM 304 Query: 293 ----GNAPKIACVSNCVAPCNRGEEAKKVG-YCIADGLGRSYLGNREEGLYFTGANGYRV 347 G K +C+ C + K G +CI + L + G+ ++GL+F GA+ Sbjct: 305 AAAAGKEHKCTLAWDCLLQCGLRDSNPKHGQFCIDNQLAAAVTGDVQKGLFFRGASSLPF 364 Query: 348 DKII-SVHELIKELTEG 363 I V EL+ L G Sbjct: 365 GSAIRPVRELMHYLLTG 381 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: 338 Number of extensions: 18 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 363 Length of database: 387 Length adjustment: 30 Effective length of query: 333 Effective length of database: 357 Effective search space: 118881 Effective search space used: 118881 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: 50 (23.9 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