Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate GFF3996 HP15_3936 acyl-CoA dehydrogenase domain protein
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Marino:GFF3996 Length = 389 Score = 236 bits (602), Expect = 9e-67 Identities = 138/385 (35%), Positives = 217/385 (56%), Gaps = 5/385 (1%) Query: 46 SDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI 105 +D F+ L E+ +R +R ++++ P +TE +F I ++G +G+ G ++ Sbjct: 7 NDLLGFDAQLDETERQVRDSIRSFCDEQLMPGITEANRHEKFDRSIFNQMGELGMLGATL 66 Query: 106 -KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLA 164 + YG PGL+ + E+ RVD++ + + V SSL M I G EA K++ LP LA Sbjct: 67 PEEYGGPGLNHVCYGLIAREVERVDSAYRSALSVQSSLVMYPIYSYGKEAMKKRILPKLA 126 Query: 165 QLNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT 224 V C+ LTEP++GSD SG+ T A KV+GG+ ++G K WI NS AD+ +++A+ Sbjct: 127 SGEYVGCFGLTEPNHGSDPSGMETRAKKVDGGYLLSGSKTWITNSPIADVCVVWAK--LD 184 Query: 225 NQINGFIVKKD-APGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKV 283 ++NGF+++++ A GL+ KI K LR + G I + VFVPDE+ L V + Sbjct: 185 GKVNGFVIEREGATGLETPKIQGKFSLRASETGSIFMDEVFVPDENHLE-VEGLKGPFSC 243 Query: 284 LAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLM 343 L +R ++W +G + + Y ERKQFG PLAA QL Q+KLV M + Sbjct: 244 LNKARFGISWGSLGAAEFCWHAARNYTLERKQFGKPLAANQLIQKKLVDMQTEITIGLQA 303 Query: 344 GWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEP 403 +L ++ + G +TP SL K KA + A + R++ GGNGI ++ V + +LE Sbjct: 304 VLQLGRMMDAGTVTPDAISLLKRNNCGKALDIARVARDMHGGNGIADEYHVIRHVMNLEA 363 Query: 404 IYTYEGTYDINTLVTGREVTGIASF 428 + TYEGT+D++ L+ GR TGI +F Sbjct: 364 VNTYEGTHDVHALILGRGQTGIQAF 388 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: 350 Number of extensions: 20 Number of successful extensions: 3 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: 389 Length adjustment: 31 Effective length of query: 405 Effective length of database: 358 Effective search space: 144990 Effective search space used: 144990 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