Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_017601818.1 D471_RS0128745 acyl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000341125.1:WP_017601818.1 Length = 384 Score = 303 bits (776), Expect = 5e-87 Identities = 168/375 (44%), Positives = 234/375 (62%), Gaps = 2/375 (0%) Query: 2 LATEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCD 61 L T E Q+ ++ R+ ++ L P AAE + FPR+A + G G+ P ++GG D Sbjct: 7 LHTPEAEQLLELTREIVDKELLPRAAEDEDNAAFPRDAFRTLGAAGLLGLPYPGEYGGGD 66 Query: 62 TGYLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAF 121 Y Y +EE+A G A +SVH ++ C P+ FG D+QKA L + G +LGA+ Sbjct: 67 QPYEIYLQVVEELARGWLAVGLGVSVH-TLSCYPVAAFGTDDQKAAHLPDMVGGDLLGAY 125 Query: 122 ALTEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTD-PSAGKRGIS 180 L+E +GSDA++L TRA Y +NG K +IT G A +FA T P +G RGIS Sbjct: 126 CLSETASGSDAAALTTRAEPVEGGYRVNGAKAWITHGGRADYYALFARTGAPDSGARGIS 185 Query: 181 AFIVPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGG 240 F VP D+PG A E K+G +S T +LF+D+++ +GE G+ IALA L+ G Sbjct: 186 CFHVPADTPGLGAAAPERKMGMSSSPTAGVLFDDVRLGADALIGERDRGFGIALAALDSG 245 Query: 241 RVGIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+GIAA AVG+A+AA +AA Y+RER FG I + Q V F LADMATQIA +R++ A Sbjct: 246 RLGIAACAVGLAQAALDAALAYSRERRQFGTAIGDFQGVGFMLADMATQIAASRELYLSA 305 Query: 301 AALRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIY 360 A LRD+G+P +A+MAKL A++ A +V + A+Q GGYGY DFP+ER R+ +V QI Sbjct: 306 ARLRDAGRPFGTQAAMAKLMATDTAMRVTTDAVQVFGGYGYTRDFPVERYMREAKVLQIV 365 Query: 361 EGTSDIQRMVISRNL 375 EGT+ +QR+VISR+L Sbjct: 366 EGTNQVQRLVISRDL 380 Lambda K H 0.320 0.134 0.388 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: 395 Number of extensions: 24 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: 384 Length adjustment: 30 Effective length of query: 345 Effective length of database: 354 Effective search space: 122130 Effective search space used: 122130 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