Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate BPHYT_RS11475 BPHYT_RS11475 2-nitropropane dioxygenase
Query= metacyc::HP0773-MONOMER (363 letters) >FitnessBrowser__BFirm:BPHYT_RS11475 Length = 396 Score = 165 bits (418), Expect = 2e-45 Identities = 121/366 (33%), Positives = 192/366 (52%), Gaps = 23/366 (6%) Query: 18 PIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERIVAKKPFEALNFYSK 77 PI QGGMGVGIS LAG+VA+EGALG I+++ ++ + +ER L + Sbjct: 19 PIVQGGMGVGISAHRLAGSVAREGALGTIASIDLRHH-HRDLMERCRESPDRATLEEANL 77 Query: 78 KALNEIFANARKIC-GNNPLGANILYAINDYGRVLRDSCEAGANIIITGAGLPTNMPEFA 136 AL +A+ + G + N++ A++ +R +CE+GA+ I+ GAGLP ++P+ Sbjct: 78 TALAREIHSAKALSEGRGMIAVNVMKAVSAQADYVRVACESGADAIVMGAGLPLDLPDMT 137 Query: 137 KDFSDVALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPL-SGGHQGF-----KYEDC 190 + + D+ALIPI+S ++ + ++ K+W + R+PDA ++E P +GGH G +++ Sbjct: 138 QGY-DIALIPILSDSRGVALVLKKWMKK-GRLPDAVVIEHPAHAGGHLGVNNLADQHDGR 195 Query: 191 FKEEFRLENLVPKVVEASKEWGNIPIIAAGGIWDRKDIDTMLSLGASGVQMATRFLGTKE 250 F LE L V ++P+I AGGI + + +L+ GASGVQ+ T F T+E Sbjct: 196 FDFLRILEELDAVFVSLGLNRQDVPLIVAGGINSHEAVRALLNAGASGVQLGTPFAVTEE 255 Query: 251 CDAKV-YADLLPTLKKEDILLIKSPVGYPARAINTGVIKRI--------EEGNAPKIACV 301 DA + +L EDI+ S G PARA+ T + R E+ A K C Sbjct: 256 GDAHPNFKRVLAEATPEDIVEFVSVTGLPARAVKTPWLMRYLRHETKIREKVGALKHICP 315 Query: 302 S--NCVAPCNRGEEAKKVG-YCIADGLGRSYLGNREEGLYFTGANGYRVDKII-SVHELI 357 + C++ C + +K G +CI L + G+ GL+F G I SVH+L+ Sbjct: 316 TALECLSACGWRDGIEKFGHFCIDTRLAAALRGDVANGLFFRGREALPFGTAIRSVHDLL 375 Query: 358 KELTEG 363 + L G Sbjct: 376 ELLLTG 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: 357 Number of extensions: 16 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: 396 Length adjustment: 30 Effective length of query: 333 Effective length of database: 366 Effective search space: 121878 Effective search space used: 121878 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