Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate 3607424 Dshi_0838 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Dino:3607424 Length = 382 Score = 247 bits (630), Expect = 4e-70 Identities = 140/376 (37%), Positives = 220/376 (58%), Gaps = 3/376 (0%) Query: 3 VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 + DE + +A+ R F P E+W +E + ELGL VPE +GG Sbjct: 7 MTDEHRMLAEMTRNFITTEWAPHFERWRDQGEMDREIWQQAGELGLLCPSVPEAYGGPGG 66 Query: 63 GYVAYAMALEEIAAGD-GACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121 + A L EIA + A +H+ + IL +G+E+QK+++L + +G M+GA Sbjct: 67 DFGHEAAILIEIARANLSAWGAGHGIHSGIVAHYILAYGSEEQKQKWLPKMVSGEMVGAL 126 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181 A+TEP AGSD +KTRA +G+ Y L+GSK FIT+GQ+A +++V A TDP AG +G+S Sbjct: 127 AMTEPGAGSDLQGIKTRAVKDGNGYRLSGSKIFITNGQHANLIVVAAKTDPSAGAKGVSL 186 Query: 182 FIVPTD-SPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAE-GEGYKIALANLEG 239 ++ T+ + G+ R K+G HASDT ++ FDNV +P N LG E G+G+ + L Sbjct: 187 VVLETEGAEGFSRGRNLHKVGMHASDTSELFFDNVAIPPENLLGGEVGKGFYQMMTQLPQ 246 Query: 240 GRIGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLH 299 R+ IA+ AVG A E YA ERQ+FG P+++ Q F+LA+ TK +VAR + Sbjct: 247 ERLIIAAGAVGAMEGAVERTVAYAKERQAFGGPILQFQNTRFKLAECQTKTTVARAFLNE 306 Query: 300 AAALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQI 359 A G+ ++ +A+MAK + ++ +V + +Q GGYGY++++ + +++ D RV +I Sbjct: 307 CMAEHLEGKLSVEKAAMAKYWITDTQGEVIDECVQLHGGYGYMAEYDIAQMWSDARVQRI 366 Query: 360 YEGTSDIQRMVIARNL 375 Y GT++I + +I R L Sbjct: 367 YGGTNEIMKELIGRAL 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: 380 Number of extensions: 18 Number of successful extensions: 4 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: 382 Length adjustment: 30 Effective length of query: 345 Effective length of database: 352 Effective search space: 121440 Effective search space used: 121440 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