Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_065400887.1 BBI00_RS21510 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_001684965.1:WP_065400887.1 Length = 452 Score = 359 bits (921), Expect = e-103 Identities = 182/429 (42%), Positives = 267/429 (62%), Gaps = 4/429 (0%) Query: 4 LSSADRASNEKKVKSSYFDLPPMEMSVAFPQATPAST---FPPCTSDYYHFNDLLTPEEQ 60 LSS + K+ ++ L ++S P PP D+Y L+PE++ Sbjct: 23 LSSISEKVDLPKLMQNFSKLDDKQLSGLMKMLDPEKKKKELPPIDGDFYDIYHTLSPEQR 82 Query: 61 AIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKGYGCPGLSITANAI 120 I+ KVR+ MEKEV P++ YW + EFPF + PK + + G + +GYGCPG+ + Sbjct: 83 EIQLKVRDFMEKEVKPLVNHYWLRDEFPFELIPKFQKLNICGVTYEGYGCPGMPFLMEGV 142 Query: 121 ATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNG 180 E+AR+DAS +TF V S L M +I +CGSE QK+K+LP + + + + LTEP+ G Sbjct: 143 IAMEMARIDASIATFFGVQSGLAMGSIYICGSEEQKQKWLPQMQKFEKIGAFGLTEPEVG 202 Query: 181 SDASG-LGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQINGFIVKKDAPGL 239 S A+G L T K GW +NGQK+WIGN+TFADL+II+AR+ + ++ GFIV+KD PG Sbjct: 203 SGAAGGLTVTCKKTPEGWILNGQKKWIGNATFADLVIIWARDLDSGEVKGFIVEKDNPGY 262 Query: 240 KATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQPIGIS 299 KI K+ LR+VQNG I L++ V +E+RL NSF+DT KVL ++R VAW G + Sbjct: 263 SVEKIKGKMALRIVQNGLITLKDCLVTEENRLQNANSFKDTGKVLRMTRAGVAWMATGCA 322 Query: 300 MGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQMTPG 359 G Y+ Y ++R+QFG P+A+FQ+ Q LV+ML N+ AM M +RL ++ + G + Sbjct: 323 RGAYESALDYTRKREQFGRPIASFQMIQGHLVEMLSNLTAMQTMVFRLSEMQDEGILKDE 382 Query: 360 QASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTLVTG 419 ASL K + + + R+ S RE++GGNGIL ++ VA+ D E IY+YEGT +IN+L+ G Sbjct: 383 HASLAKVFCTLRTRDIVSRAREVMGGNGILLEYDVARFVADAEAIYSYEGTKEINSLIVG 442 Query: 420 REVTGIASF 428 R +TG ++F Sbjct: 443 RSITGFSAF 451 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: 483 Number of extensions: 18 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: 452 Length adjustment: 32 Effective length of query: 404 Effective length of database: 420 Effective search space: 169680 Effective search space used: 169680 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: 51 (24.3 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