Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate Dsui_3369 Dsui_3369 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__PS:Dsui_3369 Length = 394 Score = 248 bits (633), Expect = 2e-70 Identities = 143/386 (37%), Positives = 214/386 (55%), Gaps = 5/386 (1%) Query: 47 DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIK 106 D +D L+ EE+ +R R+ + + P + + + + I +LG +G+ G ++ Sbjct: 8 DPLQLDDQLSAEERQVRDTARQYSQDRLLPRIVQAFRHEQTDPAIFRELGELGLLGATLD 67 Query: 107 GYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQL 166 GYGC G S + + EI RVD+ + + V SSL M I GSEA KE+ LP +A Sbjct: 68 GYGCAGASYVSYGLLAREIERVDSGYRSMVSVQSSLAMYPIHAFGSEALKERLLPKMATG 127 Query: 167 NTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTT 223 + C+ LTEP++GSD + + A V GGW++ G K WI NS AD+ +++A+ + Sbjct: 128 ELIGCFGLTEPNHGSDPGSMESRAEAVPGGWELTGAKMWITNSPIADVFVVWAKDGQDED 187 Query: 224 TNQINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKV 283 +I GF+++K GL A I K+GLR G+I++ VFVP+E+ LP V + Sbjct: 188 GGEIRGFVLEKGMKGLSAPVIQGKMGLRASVTGEIVMDKVFVPEENLLPKVKGLKGPFAC 247 Query: 284 LAVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLM 343 L +R +AW +G + + +Y +R QFG PLAA QL Q+KL M + A+ L Sbjct: 248 LNQARYGIAWGALGAAEACWHAARQYTLDRPQFGRPLAANQLVQKKLADMQTEI-ALGLQ 306 Query: 344 G-WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLE 402 G RL +L + G+ P SL K KA E A R++ GGNGI +F V + +LE Sbjct: 307 GCLRLGRLKDEGKDAPEMTSLLKRNSCGKALEIARTARDMHGGNGISDEFHVVRHMLNLE 366 Query: 403 PIYTYEGTYDINTLVTGREVTGIASF 428 + TYEGT+DI+ L+ GR TGIA+F Sbjct: 367 VVNTYEGTHDIHALILGRAQTGIAAF 392 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: 367 Number of extensions: 14 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: 394 Length adjustment: 31 Effective length of query: 405 Effective length of database: 363 Effective search space: 147015 Effective search space used: 147015 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 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