Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_007155433.1 MDG893_RS18850 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_000170835.1:WP_007155433.1 Length = 389 Score = 220 bits (560), Expect = 7e-62 Identities = 131/384 (34%), Positives = 208/384 (54%), Gaps = 5/384 (1%) Query: 47 DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105 D F+ L E+ +R +R ++ + P +TE +F I +G +G+ G ++ Sbjct: 8 DLLQFDKQLDETERQVRDSIRSFCDQRLMPGITEANRHEKFDRSIFTDMGELGMLGATLP 67 Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165 + YG PGL+ + E+ RVD++ + + V SSL + I G EA K++ LP LA Sbjct: 68 EEYGGPGLNHVCYGLIAREVERVDSAYRSALSVQSSLVIHPIHAFGQEALKKRILPQLAS 127 Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225 V C+ LTEP++GSD + T A KV+GG+ ++G K WI NS AD+ +++A+ Sbjct: 128 GEKVGCFGLTEPNHGSDPGNMETRAKKVDGGYLVSGSKTWITNSPIADVCVVWAK--LEG 185 Query: 226 QINGFIVKKD-APGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVL 284 +I GF+++++ A GL KI K LR + G I + VFVPDE++L V + L Sbjct: 186 KITGFVIEREGAKGLDTPKIEGKFSLRASETGSIFMDEVFVPDENKL-DVEGLKGPFSCL 244 Query: 285 AVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMG 344 +R ++W +G + + Y ERKQFG PLAA QL Q+KL M + Sbjct: 245 NKARFGISWGSLGAAEFCWHAALNYTLERKQFGKPLAANQLIQKKLADMQTEITLGLQGA 304 Query: 345 WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPI 404 +L ++ + G + S+ K KA + A + R++ GGNGI ++ V + +LE + Sbjct: 305 LQLGRMIDAGNYSTDAISMLKRNNCGKALDIARVARDMHGGNGIADEYHVIRHVMNLEAV 364 Query: 405 YTYEGTYDINTLVTGREVTGIASF 428 TYEGT+D++ L+ GR TGI +F Sbjct: 365 NTYEGTHDVHALILGRGQTGIQAF 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: 347 Number of extensions: 14 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 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