Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate Echvi_1473 Echvi_1473 Acyl-CoA dehydrogenases
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Cola:Echvi_1473 Length = 380 Score = 323 bits (828), Expect = 5e-93 Identities = 160/372 (43%), Positives = 241/372 (64%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 T+ Q I+ R F + + PF EWD FP ++ ELG G+L+P ++GG G Sbjct: 7 TENQSMIAQMIRDFGAKEITPFRKEWDDHQTFPLPLFKKLGELGLMGVLIPSEYGGSGFG 66 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 YL Y A+ E+A D M+ HNS+ I+ FG+++QK+++L LAS LGA+ L Sbjct: 67 YLEYVTAILELAKLDPGIGLSMAAHNSLCSGHIMLFGSEEQKQKYLPKLASCEFLGAWGL 126 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP GSDA+++KT A GD++VLNG K FIT G + V +V A T K G++AF+ Sbjct: 127 TEPNTGSDAANMKTTATAEGDYFVLNGAKNFITHGVSGDVAVVIARTGEVGDKHGMTAFV 186 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 V + G++ R EDKLG S+T +++FED +V + LGE GEG+ ++ L+GGR+ Sbjct: 187 VEKGTEGFRGGRKEDKLGMRTSETAELIFEDCRVHKSQILGEVGEGFIQSMKVLDGGRIS 246 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IA+ S+G+A AFEAA Y++ER+ F KPI +Q ++F+LADMAT++ A+ + AA L Sbjct: 247 IAALSLGIAEGAFEAALSYSKERQQFQKPISAYQGISFKLADMATKLEAAKLLTFKAADL 306 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 ++ G+ + ++ AK +ASE+A ++ + A+Q GGYG+ D+P+E+ YRDV++C I EGT Sbjct: 307 KNRGEYVTLASAQAKYYASEIAVELANEAVQVYGGYGFTKDYPVEKYYRDVKLCTIGEGT 366 Query: 364 SDIQRMVISRNL 375 S+IQ++VISR L Sbjct: 367 SEIQKIVISREL 378 Lambda K H 0.319 0.134 0.389 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: 333 Number of extensions: 11 Number of successful extensions: 1 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: 380 Length adjustment: 30 Effective length of query: 345 Effective length of database: 350 Effective search space: 120750 Effective search space used: 120750 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 Apr 09 2024. 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