Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_039790199.1 CEJ45_RS12595 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_002213425.1:WP_039790199.1 Length = 394 Score = 160 bits (404), Expect = 9e-44 Identities = 116/381 (30%), Positives = 181/381 (47%), Gaps = 27/381 (7%) Query: 61 AIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGLSITANA 119 A+R+ V + E+AP E +FP + KLG +GV G ++ + YG GL A+ Sbjct: 17 ALREAVAAFAQTEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVGEEYGGAGLGYLAHI 76 Query: 120 IATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDN 179 IA EI+R AS HS+L + I G+E QK KYLP L + + A++EP+ Sbjct: 77 IAMEEISRASASVGLSYGAHSNLCVNQIKRNGNEEQKRKYLPKLISGDFIGALAMSEPNA 136 Query: 180 GSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTNQINGFIVKKDA 236 GSD + A K + +NG K WI N AD+L+++A+ + + F+V+K Sbjct: 137 GSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADVLVVYAKTDLDAGARGMTAFLVEKGY 196 Query: 237 PGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGV-NSFQDTSKVLAVSRVMVAWQP 295 G + +K+G+R G+++ Q+ VP+E+ L GV L R +++ P Sbjct: 197 KGFSVAQKLDKLGMRGSHTGELVFQDCEVPEENVLGGVGRGVNVLMSGLDFERSVLSGGP 256 Query: 296 IGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCK--LYET 353 +GI D+ Y+ +RKQFG + FQL Q KL M + A CK +Y Sbjct: 257 LGIMQACMDVVVPYVHDRKQFGQAIGEFQLMQGKLADMYSTMMA--------CKAYVYAV 308 Query: 354 GQMTPGQASLGKA------------WISSKARETASLGRELLGGNGILADFLVAKAFCDL 401 GQ S K + + KA A + LGGNG + ++ V + + D Sbjct: 309 GQACDRADSADKVRALRKDAAGAILYSAEKATWMAGEAIQSLGGNGYINEYPVGRLWRDA 368 Query: 402 EPIYTYEGTYDINTLVTGREV 422 + GT +I ++ GRE+ Sbjct: 369 KLYEIGAGTSEIRRMLIGREL 389 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: 385 Number of extensions: 23 Number of successful extensions: 5 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: 394 Length adjustment: 31 Effective length of query: 405 Effective length of database: 363 Effective search space: 147015 Effective search space used: 147015 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