Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate RR42_RS08770 RR42_RS08770 2-nitropropane dioxygenase
Query= metacyc::HP0773-MONOMER (363 letters) >FitnessBrowser__Cup4G11:RR42_RS08770 Length = 393 Score = 155 bits (393), Expect = 1e-42 Identities = 112/366 (30%), Positives = 186/366 (50%), Gaps = 24/366 (6%) Query: 18 PIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKN--MRFVERIVAKKPFEALNFY 75 P+ QGGMG+GIS LAG VA + +G I+++ ++ + + K EA N Sbjct: 15 PVVQGGMGIGISAHRLAGAVASQNGMGTIASIDLRHHHPDLLAATAKSRDKAKTEAANLV 74 Query: 76 SKKALNEIFANARKICGNN-PLGANILYAINDYGRVLRDSCEAGANIIITGAGLPTNMPE 134 AL+ AR++ G + N++ A++ + ++R +CE+GA+ I+ GAGLP ++PE Sbjct: 75 ---ALDREIQGARRLSGGRGAIAVNVMKAVSSHAALVRQACESGADAIVMGAGLPLDLPE 131 Query: 135 FAKDFSDVALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPL-SGGHQG-FKYEDCFK 192 ++ALIPI+S ++ + ++ ++W + R+PDA +VE P +GGH G + ED Sbjct: 132 LTAGHPNIALIPILSDSRGIGLVLRKWMKK-NRLPDAIVVEHPAHAGGHLGASRIEDLGD 190 Query: 193 EEFRLENLVPKVVE----ASKEWGNIPIIAAGGIWDRKDIDTMLSLGASGVQMATRFLGT 248 + F ++ + E W ++P+I AGGI + L GA+ VQ+ T F T Sbjct: 191 QRFSFTRVLAECRELFAGLGLAWDSVPLILAGGINTHAKVRHWLDQGAAAVQLGTAFAVT 250 Query: 249 KECDA-KVYADLLPTLKKEDILLIKSPVGYPARAINTGVIKRIEEGNA-----PKIA-CV 301 +E DA + ++L + + S G PARA+ T +KR A K+ C+ Sbjct: 251 EEGDAHPAFKEVLASAHPGQLSEFTSVAGLPARAVLTPWLKRYLSREAALQTRAKVRDCL 310 Query: 302 S--NCVAPCNRGEEAKKVG-YCIADGLGRSYLGNREEGLYFTGANGYRVDKII-SVHELI 357 +C+ C + +VG +CI L ++ G+ E GL+F G + I V EL+ Sbjct: 311 EGFDCLQACGLRDGVGRVGQFCIDLKLAQAMRGDVERGLFFRGKGALPFGEAIRPVRELM 370 Query: 358 KELTEG 363 L G Sbjct: 371 HYLLTG 376 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: 356 Number of extensions: 28 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: 393 Length adjustment: 30 Effective length of query: 333 Effective length of database: 363 Effective search space: 120879 Effective search space used: 120879 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