Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Dsui_3369 Dsui_3369 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__PS:Dsui_3369 Length = 394 Score = 194 bits (494), Expect = 3e-54 Identities = 124/368 (33%), Positives = 189/368 (51%), Gaps = 2/368 (0%) Query: 6 EQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGYV 65 E++Q+ D R ++Q+RL P Q + + E+ ELGL G + + +G + YV Sbjct: 19 EERQVRDTARQYSQDRLLPRIVQAFRHEQTDPAIFRELGELGLLGATL-DGYGCAGASYV 77 Query: 66 AYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALTE 125 +Y + EI D +++SV +S+ PI FG+E KE+ L +ATG ++G F LTE Sbjct: 78 SYGLLAREIERVDSGYRSMVSVQSSLAMYPIHAFGSEALKERLLPKMATGELIGCFGLTE 137 Query: 126 PQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAFIVP 185 P GSD S+++RA + L G+K +IT+ A V +V+A + I F++ Sbjct: 138 PNHGSDPGSMESRAEAVPGGWELTGAKMWITNSPIADVFVVWAKDGQDEDGGEIRGFVLE 197 Query: 186 TDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRIGIA 245 G ++ K+G AS T +IV D V VP N L + +G K A L R GIA Sbjct: 198 KGMKGLSAPVIQGKMGLRASVTGEIVMDKVFVPEENLL-PKVKGLKGPFACLNQARYGIA 256 Query: 246 SQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAALRD 305 A+G A A + AR Y +R FG+PL +Q V +LADM T+I++ Q L L+D Sbjct: 257 WGALGAAEACWHAARQYTLDRPQFGRPLAANQLVQKKLADMQTEIALGLQGCLRLGRLKD 316 Query: 306 AGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSD 365 G+ A S+ K + A ++ A GG G +F + R ++ V YEGT D Sbjct: 317 EGKDAPEMTSLLKRNSCGKALEIARTARDMHGGNGISDEFHVVRHMLNLEVVNTYEGTHD 376 Query: 366 IQRMVIAR 373 I +++ R Sbjct: 377 IHALILGR 384 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: 345 Number of extensions: 26 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: 394 Length adjustment: 30 Effective length of query: 345 Effective length of database: 364 Effective search space: 125580 Effective search space used: 125580 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