Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_011385596.1 AMB_RS16315 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_000009985.1:WP_011385596.1 Length = 392 Score = 233 bits (594), Expect = 8e-66 Identities = 136/384 (35%), Positives = 209/384 (54%), Gaps = 2/384 (0%) Query: 47 DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105 D + D L+ +E+ IR ++++ P + + + F I ++G MG+ G +I Sbjct: 8 DPFLLEDQLSEDEKLIRDSAHAYCQEKLQPRVMKAFRDETFDREIMNEMGEMGLLGPTIP 67 Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165 + YG PG++ A + + E+ RVD+ + + V SSL M I G+E QK+KYLP LA Sbjct: 68 EEYGGPGVNHVAYGLISREVERVDSGYRSAMSVQSSLVMHPIFSYGTEEQKKKYLPRLAT 127 Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTT-T 224 + C+ LTEPD GSD G+ T A KV+GG+ + G K WI NS +D+ I++A++ Sbjct: 128 GEIIGCFGLTEPDAGSDPGGMRTRAKKVDGGYLLTGSKMWITNSPISDIAIVWAKSDAHE 187 Query: 225 NQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVL 284 +I GFIV+K G KI K+ LR G+I+L FVPDE +P + L Sbjct: 188 GKIKGFIVEKGIKGFTTPKIEGKLSLRASITGEIVLDEAFVPDEALMPNASGLGGPFGCL 247 Query: 285 AVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMG 344 +R +AW IG + + +Y+ +RKQFG PLAA Q+ Q KL M+ + Sbjct: 248 NKARYGIAWGVIGAAEFCWHAARQYMLDRKQFGRPLAANQIPQLKLANMMTEITLGLQAC 307 Query: 345 WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPI 404 R+ ++ + P SL K KA + A + R++ GGNGI +F V + +LE + Sbjct: 308 VRVGRMMDDHTWAPEAVSLIKRNNCGKALDIARMARDMHGGNGISEEFHVIRHMVNLETV 367 Query: 405 YTYEGTYDINTLVTGREVTGIASF 428 TYEG +D++ L+ GR +TGI +F Sbjct: 368 NTYEGAHDVHALILGRAMTGIQAF 391 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: 368 Number of extensions: 17 Number of successful extensions: 2 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: 392 Length adjustment: 31 Effective length of query: 405 Effective length of database: 361 Effective search space: 146205 Effective search space used: 146205 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