Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate GFF2715 PS417_13850 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__WCS417:GFF2715 Length = 375 Score = 352 bits (902), Expect = e-101 Identities = 172/359 (47%), Positives = 248/359 (69%) Query: 18 FAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSR 77 FA+ +KP A E D E RFP E + +MA+ G G+ P+++GG + Y MA+EE++ Sbjct: 17 FAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAMALEEIAA 76 Query: 78 VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQ 137 G I+S H S+G P+ ++GN++QK++FL+PLASG LGAF LTEP AG+DAS + Sbjct: 77 GDGACSTIMSVHNSVGCVPVLKFGNDQQKEQFLKPLASGAMLGAFALTEPQAGSDASSLK 136 Query: 138 TTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTPGFSFGVK 197 T A L+GD Y+LNG K FIT+ + +V A+TD + G +GISAFIV +PG+S Sbjct: 137 TRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPAAGKRGISAFIVPTDSPGYSVARV 196 Query: 198 EKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGAL 257 E K+G S T +++FED ++P N LG+EG+G+KIA++ L+GGR+GIA+QA+G+A+ A Sbjct: 197 EDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGGRVGIASQAVGMARAAF 256 Query: 258 DETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVEAAM 317 + Y +ER FG+P+ + Q F+LADM ++ AR +V+ AA +D GKP VEA+M Sbjct: 257 EAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKPALVEASM 316 Query: 318 AKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGKL 376 AKLFA+E A +V + A+Q GGYGY D+P+ER+ RD ++ +IYEGTS++QRMVIS L Sbjct: 317 AKLFASEMAEKVCSAALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRMVISRNL 375 Lambda K H 0.315 0.133 0.373 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: 357 Number of extensions: 13 Number of successful extensions: 1 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: 378 Length of database: 375 Length adjustment: 30 Effective length of query: 348 Effective length of database: 345 Effective search space: 120060 Effective search space used: 120060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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