Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__SB2B:6938693 Length = 391 Score = 221 bits (563), Expect = 3e-62 Identities = 135/383 (35%), Positives = 203/383 (53%), Gaps = 3/383 (0%) Query: 47 DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105 D +FN LLT EE+ IR V E + ++ + F I +LG +G+ G ++ Sbjct: 10 DPLNFNSLLTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGELGLLGATLP 69 Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165 + YGC + + + EI RVD+ + + V SSL M I G+EAQ+ KYLP LA Sbjct: 70 EEYGCANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQRRKYLPKLAT 129 Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225 V C+ LTEPD GSD +G+ T A +++GG++I G K WI NS AD+ +++A+ Sbjct: 130 GEWVGCFGLTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFVVWAK--LDG 187 Query: 226 QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLA 285 I GF+++K GL A KI K LR G+I++ NV V ++ LP V + L Sbjct: 188 AIRGFVLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEDALLPNVEGLKGPFGCLN 247 Query: 286 VSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGW 345 +R +AW +G + + +Y +R QF PLAA QL Q+KL M + Sbjct: 248 KARYGIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEITTGLFACL 307 Query: 346 RLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIY 405 + +L + + SL K KA + A + R++ GGNGI +F V + +LE + Sbjct: 308 QAGRLMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRHVMNLEAVN 367 Query: 406 TYEGTYDINTLVTGREVTGIASF 428 TYEGT+DI+ L+ GR T + +F Sbjct: 368 TYEGTHDIHALILGRAQTDLQAF 390 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: 326 Number of extensions: 13 Number of successful extensions: 3 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: 391 Length adjustment: 31 Effective length of query: 405 Effective length of database: 360 Effective search space: 145800 Effective search space used: 145800 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 Apr 09 2024. 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