Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_011383120.1 AMB_RS03480 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_000009985.1:WP_011383120.1 Length = 389 Score = 166 bits (421), Expect = 9e-46 Identities = 112/366 (30%), Positives = 177/366 (48%), Gaps = 5/366 (1%) Query: 62 IRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGLSITANAI 120 +R V E+AP E EFP + P+LGAMG+ G ++ + YG G+ + + Sbjct: 19 MRDSVAAFAATEIAPRAAEIDRSNEFPNELWPRLGAMGLLGITVDEKYGGAGMGYLEHVV 78 Query: 121 ATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNG 180 A EI+R AS HS+L + I G+EAQK KYLP L + A++EP+ G Sbjct: 79 AMEEISRASASVGLSYGAHSNLCVNQIKRNGTEAQKMKYLPKLISGEYIGALAMSEPNAG 138 Query: 181 SDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTT---NQINGFIVKKDAP 237 SD + A K + +NG K WI N AD+++++A+ T I F+V+K Sbjct: 139 SDVVSMKLKAEKKGDRYVLNGTKMWITNGPDADVIVVYAKTDVTAGPRGITAFLVEKTFK 198 Query: 238 GLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDT-SKVLAVSRVMVAWQPI 296 G + +K+G+R G+++ Q+ VP+E+ L V + L RV++ P+ Sbjct: 199 GFSVAQKLDKLGMRGSNTGELVFQDCEVPEENVLGAVGKGVNVLMSGLDYERVVLTGGPL 258 Query: 297 GISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQM 356 GI D+ Y+ ER QFG P+ FQL Q KL M A + + K + G+ Sbjct: 259 GIMAACMDVVVPYVHERTQFGQPIGTFQLMQGKLADMYTTFNACRAYTYAVAKACDRGET 318 Query: 357 TPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTL 416 + A+ + + KA A + LGGNG + ++ + D + GT +I + Sbjct: 319 SRKDAAGVILYGAEKATWMALEAIQTLGGNGYINEYATGRLLRDAKLYEIGAGTSEIRRM 378 Query: 417 VTGREV 422 + GRE+ Sbjct: 379 LIGREL 384 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: 363 Number of extensions: 20 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: 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