Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_058857968.1 AS188_RS05245 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_001482365.1:WP_058857968.1 Length = 412 Score = 286 bits (731), Expect = 1e-81 Identities = 140/364 (38%), Positives = 226/364 (62%) Query: 65 KVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKGYGCPGLSITANAIATAE 124 + R +E+++ P++ E+W++AE+ + +LG + + + G +S TA + E Sbjct: 48 RARAFVEEDLLPVIGEHWDRAEYSLDLVRRLGELDLLRDGVAVEGFAPMSKTAAGLVCME 107 Query: 125 IARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTEPDNGSDAS 184 ++R D S +T V L M +IA+CG+E Q++++LP +A + +ALTEP +GSD+ Sbjct: 108 LSRGDGSIATVTGVQGGLAMRSIAMCGTEEQRQRWLPRMATGELLGAFALTEPTHGSDSV 167 Query: 185 GLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTNQINGFIVKKDAPGLKATKI 244 GL T A+ VEGGW +NG+K+WIGN + + +++AR+ +++GF+V +++ G T I Sbjct: 168 GLETRASPVEGGWLLNGEKKWIGNGSMGGITVVWARSDADGRVHGFVVPQESEGYTGTTI 227 Query: 245 PNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMVAWQPIGISMGIYD 304 P K+ LR + I +NVFVP+E+ LP SF+DT+ VL +R+ VAW +G + Y+ Sbjct: 228 PGKLALRAIHQAHIRFENVFVPEENVLPAARSFKDTAAVLFATRIGVAWGAVGHAQACYE 287 Query: 305 MCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYETGQMTPGQASLG 364 +Y +R QFG PLAA Q+ Q++L +ML + + L+ R+ + E G +T QASL Sbjct: 288 SAVQYAAQRVQFGRPLAASQIVQERLARMLSELTQIQLLVARMTEREEAGTLTAEQASLA 347 Query: 365 KAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYDINTLVTGREVTG 424 K + AR A+ R+LLGGNGIL VA+ F D+E ++TYEGT + L+ GR +TG Sbjct: 348 KYTATRAARSIAANARDLLGGNGILVRHRVARHFADVEALHTYEGTETVQALIVGRGITG 407 Query: 425 IASF 428 I++F Sbjct: 408 ISAF 411 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: 391 Number of extensions: 11 Number of successful extensions: 1 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: 412 Length adjustment: 32 Effective length of query: 404 Effective length of database: 380 Effective search space: 153520 Effective search space used: 153520 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