Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_058929012.1 AU252_RS00305 acyl-CoA dehydrogenase family protein
Query= BRENDA::B0EVL5 (395 letters) >NCBI__GCF_001484605.1:WP_058929012.1 Length = 400 Score = 266 bits (681), Expect = 6e-76 Identities = 151/390 (38%), Positives = 228/390 (58%), Gaps = 7/390 (1%) Query: 11 ADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATI 70 +D LD LT E +RD RA++++R+LP + E + + + + ELG++G TI Sbjct: 12 SDYFRLDDDLTPEEIGIRDKVRAFAEQRVLPVINEYWEKAEFPTVLLPPLAELGIIG-TI 70 Query: 71 PEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLA 130 + YG GM+ G++ARE+ R D + + + S+L M +N GS+E K+++LP LA Sbjct: 71 IQGYGCPGMSRKAAGMVAREMARADGSLNTFLGIHSNLCMGALNILGSDEQKERWLPALA 130 Query: 131 TGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKD-DA 189 E G F LTEP+HGSD ++ T AR+ + L+G K WI N +ADV V++A++ + Sbjct: 131 RIEKTGAFALTEPDHGSDSVALETSARRDGDHWVLNGHKRWIGNGHVADVIVLFARNTED 190 Query: 190 GDIRGFVLEKGWKG-----LSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKG 244 G++ FV+EK G S I GKVG RA + +IV++E+ P N + Sbjct: 191 GNVNAFVIEKDDDGRYPAGYSPTVITGKVGKRAILQADIVIEEMRLPAANRLEGCHSFRD 250 Query: 245 PFTCLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITL 304 L + R G AW A+G A A +E A Y R QFG+P+A+ QL+Q +LA+ML+E+T Sbjct: 251 VSRVLQATRGGAAWEAVGHAMAAFEIASDYAQTRIQFGKPIASYQLVQSRLANMLSELTT 310 Query: 305 GLQGCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLV 364 C R+ L D G V S++K + K I AR++LGGNG+ E + RH+ Sbjct: 311 MQLLCNRMAELADRGQLTVAQASMVKMATAQKGKWICNEARELLGGNGLLLENHVIRHMT 370 Query: 365 NLEVVNTYEGTHDIHALILGRAITGLAAFS 394 ++EVV+TYEGT + ALI+GR ITG++AF+ Sbjct: 371 DMEVVSTYEGTDSMQALIVGRDITGISAFN 400 Lambda K H 0.319 0.136 0.409 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: 356 Number of extensions: 16 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: 395 Length of database: 400 Length adjustment: 31 Effective length of query: 364 Effective length of database: 369 Effective search space: 134316 Effective search space used: 134316 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 (21.8 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