Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate WP_012991556.1 THAL_RS02560 nitronate monooxygenase
Query= metacyc::HP0773-MONOMER (363 letters) >NCBI__GCF_000025605.1:WP_012991556.1 Length = 385 Score = 398 bits (1022), Expect = e-115 Identities = 200/361 (55%), Positives = 268/361 (74%), Gaps = 6/361 (1%) Query: 5 LKPLKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERIV 64 L LKIGK ++ PI QGGMGVGISW++LAG VA+EGA+GV+SAVGTGY + V+R Sbjct: 2 LPELKIGKIRLEIPIIQGGMGVGISWEKLAGAVAREGAMGVVSAVGTGY-RFPELVKRDK 60 Query: 65 AKKPFEALNFYSKKALNEIFANARKICGNN-PLGANILYAINDYGRVLRDSCEAGANIII 123 +P ++ +SK+AL + A++I N +G NIL AI DYGRV++D+ EAGA+ II Sbjct: 61 FGRPIGSVYTHSKEALTILIKEAKRISQNRGAIGVNILCAITDYGRVVQDAIEAGADAII 120 Query: 124 TGAGLPTNMPEFAKDFSDVALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPLSGGHQ 183 +GAGLP +PE+A+ SDVALIPI+SSA+AL ++C+ W +YKR+PDA I+EGP SGGHQ Sbjct: 121 SGAGLPLRLPEYAEG-SDVALIPIVSSARALNLICRTWEKKYKRLPDAVILEGPKSGGHQ 179 Query: 184 GFKYEDCFKEEFRLENLVPKVVEASKEWGNIPIIAAGGIWDRKDIDTMLSLGASGVQMAT 243 GFKYE+CF E++LENL P ++E + WG IP+I AGG+W +DI + GA GVQ+AT Sbjct: 180 GFKYEECFMPEYQLENLFPSLLEEANRWGGIPVIVAGGVWSYQDIKWYIDRGAKGVQIAT 239 Query: 244 RFLGTKECDA-KVYADLLPTLKKEDILLIKSPVGYPARAINTGVIKRIEEGNAPKIACVS 302 RF+ T ECDA +Y ++L ++EDI+L+KSPVGYP R + T ++R+ EG CVS Sbjct: 240 RFIATHECDAPPIYKEILLKAEEEDIILLKSPVGYPLRVVKTPFVERLLEGYNGWQGCVS 299 Query: 303 NCVAPCNRGEEAKKVGYCIADGLGRSYLGNREEGLYFTGANGYRVDK--IISVHELIKEL 360 +CV PCN+GEEAKKVG+CIAD LG ++LGN EEGL+ +GANG+ + K IISV EL++ L Sbjct: 300 HCVVPCNKGEEAKKVGFCIADRLGAAWLGNYEEGLFISGANGHLLKKQGIISVKELLEIL 359 Query: 361 T 361 T Sbjct: 360 T 360 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: 491 Number of extensions: 21 Number of successful extensions: 4 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: 385 Length adjustment: 30 Effective length of query: 333 Effective length of database: 355 Effective search space: 118215 Effective search space used: 118215 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 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