Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_111393848.1 CLV31_RS15640 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_003253485.1:WP_111393848.1 Length = 401 Score = 251 bits (641), Expect = 3e-71 Identities = 138/384 (35%), Positives = 209/384 (54%), Gaps = 2/384 (0%) Query: 47 DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIK 106 D+ +DLLT E++ IR +R+ ++KE++P + ++ +KA FP+ I K G +G G + Sbjct: 19 DFLDLDDLLTEEQKLIRSSIRDFVKKEISPYIEDWAQKAHFPYEIVKKFGEVGAFGPQLP 78 Query: 107 -GYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165 YGC GL + + EI R D+ + V SL M I G+E Q+ KYLP LA Sbjct: 79 VEYGCGGLDYISYGLIMQEIERGDSGMRSTASVQGSLVMYPIYKFGTEEQRLKYLPRLAS 138 Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225 + C+ LTEPD+GS+ SG+ T + + +NG K WI NS AD+ +++A+N Sbjct: 139 GELLGCFGLTEPDHGSNPSGMVTNFKDMGDHYLLNGAKMWISNSPKADIAVVWAKNEE-G 197 Query: 226 QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLA 285 +I G IV++ G + NK LR G+++ NV VP E+ LPG L Sbjct: 198 RIQGLIVERGMEGFSTPETHNKWSLRASCTGELVFDNVKVPKENLLPGKTGLGAPMMCLD 257 Query: 286 VSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGW 345 +R +AW IG +M Y+ RY ER QFG P+ FQL Q+KL +ML + L+ W Sbjct: 258 SARFGIAWGAIGAAMDCYESARRYAAERIQFGKPIGGFQLTQKKLAEMLTEITKAQLLAW 317 Query: 346 RLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIY 405 ++ K+ G+ S+ K A A R++ GG GI ++ + + +LE + Sbjct: 318 KVGKMMNEGKAKTVHISMAKRNNVEMALNIAREARQIHGGMGITGEYPIMRHMMNLESVI 377 Query: 406 TYEGTYDINTLVTGREVTGIASFK 429 TYEGT+DI+ L+ G E+TGI +FK Sbjct: 378 TYEGTHDIHLLILGNEITGIQAFK 401 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: 375 Number of extensions: 15 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: 401 Length adjustment: 32 Effective length of query: 404 Effective length of database: 369 Effective search space: 149076 Effective search space used: 149076 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