Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate CA265_RS22715 CA265_RS22715 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Pedo557:CA265_RS22715 Length = 379 Score = 179 bits (454), Expect = 1e-49 Identities = 118/378 (31%), Positives = 188/378 (49%), Gaps = 7/378 (1%) Query: 50 HFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGY 108 HF L+ E+ IR+ R+ ++E+ P + E E +FP KLG +G G + + Y Sbjct: 2 HFE--LSEEQLMIRQAARDFAQQELKPGVIERDEHQKFPAEQVKKLGELGFLGMMVSEKY 59 Query: 109 GCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNT 168 GL + + E++++DAS S + V++SL + GSEAQKEKYL LA Sbjct: 60 NGSGLDAISYVLVMEELSKIDASASVVVSVNNSLVCYGLEAYGSEAQKEKYLKPLAAGEK 119 Query: 169 VACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTN 225 + + L+EP+ GSDA+ TTA + +NG K WI N + A ++ A+ Sbjct: 120 IGAFCLSEPEAGSDATSQRTTAEDKGDYYLLNGTKNWITNGSTASTYLVIAQTHPELRHK 179 Query: 226 QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVN-SFQDTSKVL 284 IN FIV+K G NK+G+R ++ +V VP E+R+ F+ K L Sbjct: 180 GINAFIVEKGMEGFTVGPKENKLGIRGSDTHSLMFNDVKVPKENRIGEDGFGFKFAMKTL 239 Query: 285 AVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMG 344 R+ +A Q +GI+ G +++ +Y KERK FG P++ Q KL M ++A L+ Sbjct: 240 EGGRIGIAAQALGIAQGAFELATQYAKERKSFGKPISEHQAIAFKLADMATQIEAARLLV 299 Query: 345 WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPI 404 ++ L + G S+ K + S A + ++ GG G + ++ V + D + Sbjct: 300 YKAAWLKDQGLPYTQAGSMAKLYASKVAMDVTIEAVQVHGGYGFVKEYHVERLMRDAKIT 359 Query: 405 YTYEGTYDINTLVTGREV 422 YEGT +I +V REV Sbjct: 360 QIYEGTSEIQKMVISREV 377 Lambda K H 0.319 0.133 0.399 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: 325 Number of extensions: 11 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: 436 Length of database: 379 Length adjustment: 31 Effective length of query: 405 Effective length of database: 348 Effective search space: 140940 Effective search space used: 140940 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