Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate GFF1551 PGA1_c15710 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Phaeo:GFF1551 Length = 406 Score = 224 bits (570), Expect = 5e-63 Identities = 131/384 (34%), Positives = 204/384 (53%), Gaps = 2/384 (0%) Query: 47 DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105 D +D L+ +E+ I R ++++ P + +E E I ++G MG+ G +I Sbjct: 22 DPLRLDDQLSEDERMIAASARSYAQEKLQPRVLNAYENEETDPEIFREMGEMGLLGTTIP 81 Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165 + YG G + + E+ RVD+ + + V SSL M I GSE Q++KYLP L+ Sbjct: 82 EQYGGLGAGYVSYGLVAREVERVDSGYRSMMSVQSSLVMYPIYAYGSEEQRQKYLPKLSS 141 Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225 + C+ LTEPD GSD +G+ T A K +GG+++ G K WI N+ AD+ +++A++ Sbjct: 142 GEWIGCFGLTEPDAGSDPAGMKTRAEKTDGGYRLTGSKMWISNAPIADVFVVWAKSEAHG 201 Query: 226 -QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVL 284 +I GF+++K GL A KI NK LR G+I++ V V D+ LP V + L Sbjct: 202 GKIRGFVLEKGMKGLSAPKIANKASLRASITGEIVMDGVEVGDDALLPHVEGLKGPFGCL 261 Query: 285 AVSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMG 344 +R ++W +G + + +Y +RKQFG PLA QL Q KL M + Sbjct: 262 NRARYGISWGAMGAAEACWHAARQYGLDRKQFGRPLANTQLFQLKLANMQTEITLGLQAS 321 Query: 345 WRLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPI 404 R+ +L + P S+ K KA E A R++ GGNGI +F V + +LE + Sbjct: 322 LRVGRLMDEANAAPEMISIVKRNNCGKALEIARHARDMHGGNGISLEFGVIRHMVNLETV 381 Query: 405 YTYEGTYDINTLVTGREVTGIASF 428 TYEGT+D++ L+ GR TG+ +F Sbjct: 382 NTYEGTHDVHALILGRAQTGLQAF 405 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: 335 Number of extensions: 19 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: 406 Length adjustment: 32 Effective length of query: 404 Effective length of database: 374 Effective search space: 151096 Effective search space used: 151096 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