Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Dsui_0975 Dsui_0975 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__PS:Dsui_0975 Length = 390 Score = 254 bits (649), Expect = 3e-72 Identities = 139/371 (37%), Positives = 215/371 (57%), Gaps = 3/371 (0%) Query: 8 QQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGYVAY 67 + + D VRAFA + + P A Q D+D+ FP + + +LGL GM E++GG+ GY+A+ Sbjct: 15 EMLRDTVRAFAAKEIAPRAAQIDRDNEFPADLWQKFGDLGLLGMTAEEEYGGTAMGYLAH 74 Query: 68 AMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALTEPQ 127 +A+EEI+ + H+++ I R G QK ++L L +G +GA A++EP Sbjct: 75 IVAMEEISRASASVGLSYGAHSNLCVNQIRRNGTAAQKAKYLPGLISGTQVGALAMSEPN 134 Query: 128 AGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAFIVPTD 187 AGSD S+K +A +GD YVLNGSK +IT+G +A ++V+A TD AG +G++AFIV Sbjct: 135 AGSDVVSMKLKAEKKGDRYVLNGSKMWITNGGDADTLVVYAKTDLNAGAKGMTAFIVEKG 194 Query: 188 SPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRIGIASQ 247 G+ DKLG S+T + FD+ +VP N LG G G K+ ++ L+ R + Sbjct: 195 FKGFSHGTHLDKLGMRGSNTFPLFFDDCEVPEENVLGGVGNGAKVLMSGLDYERAVLCGG 254 Query: 248 AVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVL---HAAALR 304 +G+ A +V Y +ER+ FG + E Q + +LADM + R V A Sbjct: 255 PLGIMAACMDVVLPYLHEREQFGTAIGEFQLMQGKLADMYSTWQATRAYVYAVGQACDRA 314 Query: 305 DAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTS 364 D R +A+ A L+++E A + DA+QTLGG GY +++P R++RD ++ +I GTS Sbjct: 315 DHARSLRKDAAGAILYSAEKATWMAGDAIQTLGGVGYTNEYPTGRLWRDAKLYEIGAGTS 374 Query: 365 DIQRMVIARNL 375 +I+RM+I R L Sbjct: 375 EIRRMLIGREL 385 Lambda K H 0.319 0.134 0.382 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: 375 Length of database: 390 Length adjustment: 30 Effective length of query: 345 Effective length of database: 360 Effective search space: 124200 Effective search space used: 124200 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 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