Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_043745120.1 AMB_RS18150 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_000009985.1:WP_043745120.1 Length = 378 Score = 303 bits (775), Expect = 7e-87 Identities = 164/373 (43%), Positives = 229/373 (61%), Gaps = 3/373 (0%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 T +Q AA FA + P AA WD E FP++ + + AELGF G+ V E GG Sbjct: 6 TPDQEAFRQAAHDFAVGEMAPHAAHWDEEGIFPEDTLRKAAELGFAGIYVGEDVGGSALS 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 L A+ EE+AA + + +S+HN + I FG+ +Q+ RFL L S ++ L Sbjct: 66 RLDAALIFEELAAACPSTAAYISIHNMAAWM-IDSFGDQEQRRRFLPDLCSMRKFASYCL 124 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP AGSDA+SL+T+A +GDHYVLNG K FI+ G + V +V T + G +GIS + Sbjct: 125 TEPNAGSDAASLRTKAERDGDHYVLNGTKAFISGGGRSDVYVVMVRTG-APGPKGISCLV 183 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 V +PG + E KLG T ++FED +VPVANR+G EG+G+KIA+ L+GGR+ Sbjct: 184 VEAGTPGLSFGKQEKKLGWKTQPTASVIFEDCRVPVANRIGAEGDGFKIAMKGLDGGRIN 243 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 I + S+G ARA E A +Y +R+ FG+ I QA F+LADMAT++ AR M+H AA Sbjct: 244 IGACSLGGARACLEHAIEYTGQRQQFGQAISAFQATQFKLADMATELEAARLMIHRAAHS 303 Query: 304 RDSGKP-ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEG 362 DS P A V +MAK A+++ V ALQ GGYGY+ ++P+ER +RD+RV QI EG Sbjct: 304 LDSKSPQATVHCAMAKRMATDVGFAVTDAALQLHGGYGYIKEYPIERYFRDLRVHQILEG 363 Query: 363 TSDIQRMVISRNL 375 +++I R++I R L Sbjct: 364 SNEIMRVIIGRAL 376 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: 375 Number of extensions: 14 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: 378 Length adjustment: 30 Effective length of query: 345 Effective length of database: 348 Effective search space: 120060 Effective search space used: 120060 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