Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Echvi_2990 Echvi_2990 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__Cola:Echvi_2990 Length = 402 Score = 232 bits (591), Expect = 2e-65 Identities = 132/374 (35%), Positives = 201/374 (53%), Gaps = 5/374 (1%) Query: 2 LVNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSD 61 L E I ++R F ++ + P+ E+W +D FP E + + E+G FG +P ++GG Sbjct: 27 LFTAEHLLIRQSLRDFVKKEVSPYIEEWAQDAHFPSEIVPKFGEIGAFGPQIPAKYGGGG 86 Query: 62 TGYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAF 121 Y++Y + ++EI GD + +SV S+ PI FG+E+Q+E+FL LA+G LG F Sbjct: 87 LDYISYGLIMQEIERGDSGMRSTVSVQGSLVMYPIHAFGSEEQREKFLPKLASGEWLGCF 146 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISA 181 LTEP GS+ L T + GDHY+LNG+K +I++ A + +V+A E G+ I Sbjct: 147 GLTEPDHGSNPGGLTTSFKDNGDHYLLNGAKMWISNAPEADIAVVWA--KDENGR--IHG 202 Query: 182 FIVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGR 241 IV G+ K AS T ++VFDNV+VP N L + G L L+ R Sbjct: 203 LIVERGMEGFTTPTTHHKWSLRASCTGELVFDNVKVPKENLLPGK-SGLSAPLMCLDAAR 261 Query: 242 IGIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAA 301 GIA A+G A +E A+ YA ER F KP+ Q V +LA+M T+I+ A+ + Sbjct: 262 YGIAWGAIGAAMDCYESAKRYAMERIQFDKPIAAFQLVQKKLAEMLTEITKAQLLAWRLG 321 Query: 302 ALRDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYE 361 L+D G+ + SMAK MA ++ +A Q GG G D+P+ R ++ YE Sbjct: 322 TLKDQGKATSAQISMAKRNNVAMALEIAREARQIHGGMGITGDYPIMRHMMNLESVITYE 381 Query: 362 GTSDIQRMVIARNL 375 GT DI +++ + + Sbjct: 382 GTHDIHLLILGQEI 395 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: 347 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: 402 Length adjustment: 30 Effective length of query: 345 Effective length of database: 372 Effective search space: 128340 Effective search space used: 128340 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