Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate WP_041929725.1 MPE_RS16000 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >NCBI__GCF_000015725.1:WP_041929725.1 Length = 391 Score = 206 bits (523), Expect = 1e-57 Identities = 128/371 (34%), Positives = 193/371 (52%), Gaps = 5/371 (1%) Query: 3 VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 ++++++ + DA +A+ ++RL P + + + EM ELGL G +PE +GG+ Sbjct: 17 LSEDERAVRDAAQAYCRDRLAPRVLEAFRHEKTDPAIFREMGELGLLGATLPEAYGGAGL 76 Query: 63 GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122 +V Y + E+ D ++MSV +S+ VPI FG E QK+++L LA G +G F Sbjct: 77 NHVCYGLVAREVERVDSGYRSMMSVQSSLVMVPIHAFGTEAQKQKYLPKLARGEWIGCFG 136 Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182 LTEP GSD SL TRAR YVL+G+K +IT+ A V +V+A D G+ I F Sbjct: 137 LTEPNHGSDPGSLATRARAVQGGYVLSGAKMWITNSPIADVFVVWAKDD--GGQ--IRGF 192 Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242 I+ G + V K+G AS T +IV D V P N E G K L R Sbjct: 193 ILDKGMKGLEAPAVHGKVGLRASLTGEIVMDEVFCPEENAF-PEVRGLKGPFTCLNSARY 251 Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302 GIA A+G A F AR Y +R FG+PL +Q + +LADM T+I++ Q L Sbjct: 252 GIAWGALGAAEDCFHRARQYVLDRPQFGRPLAANQLIQKKLADMQTEITLGLQGCLRLGR 311 Query: 303 LRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362 ++D G A+ S+ K + + ++ A +GG G +F + R ++ V YEG Sbjct: 312 MKDEGTAAVEITSIMKRNSCGKSLEIARMARDMMGGNGISDEFGVARHLVNLEVVNTYEG 371 Query: 363 TSDIQRMVIAR 373 T D+ +++ R Sbjct: 372 THDVHALILGR 382 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: 354 Number of extensions: 15 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: 391 Length adjustment: 30 Effective length of query: 345 Effective length of database: 361 Effective search space: 124545 Effective search space used: 124545 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 24 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