Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate 351414 BT1886 conserved hypothetical protein (NCBI ptt file)
Query= metacyc::HP0773-MONOMER (363 letters) >FitnessBrowser__Btheta:351414 Length = 365 Score = 234 bits (596), Expect = 4e-66 Identities = 138/365 (37%), Positives = 203/365 (55%), Gaps = 23/365 (6%) Query: 2 VSTLKPLKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVE 61 + +K IG IK P+ QGGMGVGIS LA VA EG +GVIS G G Sbjct: 6 IKYMKSFFIGNIEIKVPVIQGGMGVGISLSGLASAVANEGGVGVISCAGLGLLY------ 59 Query: 62 RIVAKKPFEALNFYSKKALNEIFANARK--ICGNNPLGANILYAINDYGRVLRDSCEAGA 119 P E Y++K ++ + RK + +G N++ A+++Y ++R + Sbjct: 60 ------PKEK-GTYTEKCISGLKEEIRKSRMKTKGIIGVNVMVALSNYADMVRTAINEKI 112 Query: 120 NIIITGAGLPTNMPEFAKDFSDVALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPLS 179 ++I +GAGLP ++P + S L+PI+SS++A KI+C +W Y +PDA +VEGP + Sbjct: 113 DVIFSGAGLPLDLPSYLTTGSITKLVPIVSSSRAAKIICDKWQKNYNYLPDAIVVEGPKA 172 Query: 180 GGHQGFKYEDCFKEEFRLENLVPKVVEAS---KEWGNIPIIAAGGIWDRKDIDTMLSLGA 236 GGH GFK E + + L+ L+P+VV + KE +IP+IAAGGI +DI + LGA Sbjct: 173 GGHLGFKKEQLQDQNYALDVLIPEVVAIAASYKEQKHIPVIAAGGISTGEDIAHFMELGA 232 Query: 237 SGVQMATRFLGTKECDA-KVYADLLPTLKKEDILLIKSPVGYPARAINTGVIKRIEEGNA 295 SGVQM + F+ T ECDA + + ++ K ED+L+I+SPVG P RAI+ I + G Sbjct: 233 SGVQMGSIFVTTLECDASETFKEVYIHSKSEDVLIIESPVGMPGRAIDGEFIHSVNNGLE 292 Query: 296 PKIACVSNCVAPCNRGEEAKKVGYCIADGLGRSYLGNREEGLYFTGANGYRVDKIISVHE 355 C +C+ C + K YCI L + GN ++G F G+N + DKI SV E Sbjct: 293 KPRKCSFHCIKTC----DYTKSPYCIIKALYNAAKGNMKKGYAFAGSNAFLADKISSVKE 348 Query: 356 LIKEL 360 ++ L Sbjct: 349 VMNTL 353 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: 394 Number of extensions: 18 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: 365 Length adjustment: 29 Effective length of query: 334 Effective length of database: 336 Effective search space: 112224 Effective search space used: 112224 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 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