Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_111395068.1 CLV31_RS21080 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_003253485.1:WP_111395068.1 Length = 452 Score = 362 bits (929), Expect = e-104 Identities = 181/388 (46%), Positives = 253/388 (65%), Gaps = 1/388 (0%) Query: 42 PPCTSDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVA 101 P D+Y L EE+ I+ KVRE ME+E+ PI +YW +AEFP HI PK+ + +A Sbjct: 64 PAINGDFYELGKSLPKEEREIQLKVREFMEREIKPIANDYWNRAEFPMHIIPKMAELNIA 123 Query: 102 GGSIKGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLP 161 G + +GYGCPG S E+ARVD S STF V S L M ++ LCGSEAQK+++LP Sbjct: 124 GLTYQGYGCPGHSALLEGFIAMEMARVDTSISTFFGVQSGLAMGSVYLCGSEAQKQEWLP 183 Query: 162 SLAQLNTVACWALTEPDNGSDASGLGTTATKVEGG-WKINGQKRWIGNSTFADLLIIFAR 220 ++ +L + + LTEP+ GS A+G TT K EG W +NGQK+WIGN+TF+D+ +I+AR Sbjct: 184 AMQKLEKIGAFGLTEPEVGSGAAGGLTTTCKREGDVWILNGQKKWIGNATFSDMTVIWAR 243 Query: 221 NTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDT 280 + NQ+ GFIV+K PG +A K+ +K+ LR VQN I L N VP+ DRL NSF+DT Sbjct: 244 DLDDNQVKGFIVRKGNPGFQAEKLKDKMALRTVQNALITLTNCEVPESDRLQSANSFKDT 303 Query: 281 SKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAM 340 +KVL ++R VAWQ +G + G Y++ Y ER+QFG P+A+FQL Q LV MLG++ AM Sbjct: 304 AKVLRMTRAGVAWQAVGCARGAYELALAYTNERQQFGRPIASFQLVQDLLVTMLGDLTAM 363 Query: 341 FLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCD 400 M +RL ++ + G++ ASL K + + + R REL GGNGIL +A+ D Sbjct: 364 QTMVFRLSQMQDQGELLDEHASLAKVFCTLRMRSIVDHARELFGGNGILLQHDIARFVAD 423 Query: 401 LEPIYTYEGTYDINTLVTGREVTGIASF 428 E +Y+YEGT +IN+L+ GR +TG ++F Sbjct: 424 AEAVYSYEGTKEINSLIVGRAITGHSAF 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: 462 Number of extensions: 16 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