Align decanoate oxidase (EC 1.3.3.6; EC 5.3.3.14) (characterized)
to candidate H281DRAFT_05174 H281DRAFT_05174 nitronate monooxygenase
Query= metacyc::HP0773-MONOMER (363 letters) >FitnessBrowser__Burk376:H281DRAFT_05174 Length = 396 Score = 168 bits (425), Expect = 3e-46 Identities = 131/384 (34%), Positives = 198/384 (51%), Gaps = 32/384 (8%) Query: 4 TLKPLKIGKHTIKFPIFQGGMGVGISWDELAGNVAKEGALGVISAVGTGYYKNMRFVERI 63 + PL I ++ PI QGGMGVGIS LAG+VA+EGALG I+++ ++ + VER Sbjct: 6 SFSPLVIRGRSL-LPIVQGGMGVGISAHRLAGSVAREGALGTIASIDLRHH-HPDLVERC 63 Query: 64 VAKKPFEALNFYSKKAL-NEIFANARKICGNNPLGANILYAINDYGRVLRDSCEAGANII 122 L + AL EI A G + N++ A++ +R +CE+GA+ I Sbjct: 64 SRPADHATLEQANLTALAREIHAAKALSEGRGMIAVNVMKAVSAQADYVRVACESGADAI 123 Query: 123 ITGAGLPTNMPEFAKDFSDVALIPIISSAKALKILCKRWSDRYKRIPDAFIVEGPL-SGG 181 + GAGLP ++PE + D+ALIPI+S ++ + ++ KRW + R+PDA ++E P +GG Sbjct: 124 VMGAGLPLDLPEMTQG-CDIALIPILSDSRGVALVLKRWMKK-GRLPDAVVIEHPAHAGG 181 Query: 182 HQGF-KYEDCFKEEFR----LENLVPKVVEASKEWGNIPIIAAGGIWDRKDIDTMLSLGA 236 H G D + F L+ L V + +P+I AGGI + + +L+ GA Sbjct: 182 HLGVANIADMNDQRFDFVRILQELDAVFVSLGLDRKQVPLILAGGINSHEAVRALLNAGA 241 Query: 237 SGVQMATRFLGTKECDA-----KVYADLLPTLKKEDILLIKSPVGYPARAINTGVIKRI- 290 +GVQ+ T F T+E DA +V AD P EDI+ S G PARA+ T + R Sbjct: 242 NGVQLGTPFAVTEEGDAHPNFKRVLADAAP----EDIVEFVSVTGLPARAVKTPWLTRYL 297 Query: 291 -------EEGNAPKIACVS--NCVAPCNRGEEAKKVG-YCIADGLGRSYLGNREEGLYFT 340 ++ A K AC + C++ C + +K G +CI L + G+ GL+F Sbjct: 298 RHESRIRDKVGALKHACPTALECLSVCGWRDGVEKFGHFCIDTRLAAALRGDVANGLFFR 357 Query: 341 GANGYRVDKII-SVHELIKELTEG 363 G I SVH+L++ L G Sbjct: 358 GKEALPFGPAIRSVHDLLELLLTG 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: 344 Number of extensions: 17 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