Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate Echvi_0738 Echvi_0738 Acyl-CoA dehydrogenases
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Cola:Echvi_0738 Length = 452 Score = 369 bits (948), Expect = e-107 Identities = 186/388 (47%), Positives = 248/388 (63%), Gaps = 1/388 (0%) Query: 42 PPCTSDYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVA 101 PP D+Y L P EQ I KVR+ MEKEV PI EYW K FP HI PK+ +G+A Sbjct: 64 PPVNGDFYSLEKTLPPHEQEIVAKVRDFMEKEVRPIANEYWNKGHFPMHIIPKMAELGIA 123 Query: 102 GGSIKGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLP 161 G + KGYGCPG S E+ARVD S STF V S L M +I +CGSE QK+++LP Sbjct: 124 GLTYKGYGCPGHSALLEGFLAMEMARVDTSISTFFGVQSGLAMGSIYVCGSEEQKQEWLP 183 Query: 162 SLAQLNTVACWALTEPDNGSDASGLGTTATKVEGG-WKINGQKRWIGNSTFADLLIIFAR 220 + +++ + + LTEP GS +G TT K EG W INGQK+WIGN+TF+D+ +I+AR Sbjct: 184 KMQKMDVIGAFGLTEPKVGSGVAGGLTTTCKREGDEWVINGQKKWIGNATFSDITVIWAR 243 Query: 221 NTTTNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDT 280 + Q+ GFIV+KD PG KI NK+ LR VQN I +++ VP+ DRL NSF+DT Sbjct: 244 DLDDQQVKGFIVRKDNPGFHPEKIENKMALRTVQNALITMKDCRVPESDRLQNANSFKDT 303 Query: 281 SKVLAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAM 340 S++L ++R VAWQ +G G Y+ RY ERKQFG P+A FQL Q LV MLG++ AM Sbjct: 304 SEILRLTRAGVAWQAVGCGRGAYEAALRYTNERKQFGRPIAGFQLVQDLLVTMLGDLTAM 363 Query: 341 FLMGWRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCD 400 M +RL K+ + G++ ASL K + + + R REL GGNGIL ++ +A+ D Sbjct: 364 QTMVYRLSKMQDAGELKDEHASLAKVFCTLRMRTIVDHSRELFGGNGILLEYDIARFVAD 423 Query: 401 LEPIYTYEGTYDINTLVTGREVTGIASF 428 E IY+YEGT +IN+L+ GR +TG ++F Sbjct: 424 AEAIYSYEGTKEINSLIVGRAITGHSAF 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: 461 Number of extensions: 13 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 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