Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate CA265_RS22715 CA265_RS22715 acyl-CoA dehydrogenase
Query= reanno::WCS417:GFF2715 (375 letters) >FitnessBrowser__Pedo557:CA265_RS22715 Length = 379 Score = 377 bits (969), Expect = e-109 Identities = 188/372 (50%), Positives = 264/372 (70%) Query: 4 NEEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 +EEQL I AAR FAQ+ LKP E D +FP E + ++ ELGF GM+V E++ G Sbjct: 6 SEEQLMIRQAARDFAQQELKPGVIERDEHQKFPAEQVKKLGELGFLGMMVSEKYNGSGLD 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPVLKFGNDQQKEQFLKPLASGAMLGAFAL 123 ++Y + +EE++ D + S ++SV+NS+ C + +G++ QKE++LKPLA+G +GAF L Sbjct: 66 AISYVLVMEELSKIDASASVVVSVNNSLVCYGLEAYGSEAQKEKYLKPLAAGEKIGAFCL 125 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPAAGKRGISAFI 183 +EP+AGSDA+S +T A +GD+Y+LNG K +IT+G A +V A T P +GI+AFI Sbjct: 126 SEPEAGSDATSQRTTAEDKGDYYLLNGTKNWITNGSTASTYLVIAQTHPELRHKGINAFI 185 Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGGRVG 243 V G++V E+KLG SDT ++F DVKVP NR+GE+G G+K A+ LEGGR+G Sbjct: 186 VEKGMEGFTVGPKENKLGIRGSDTHSLMFNDVKVPKENRIGEDGFGFKFAMKTLEGGRIG 245 Query: 244 IASQAVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IA+QA+G+A+ AFE A YA+ER+SFGKPI EHQA+AF+LADMATQI AR +V+ AA L Sbjct: 246 IAAQALGIAQGAFELATQYAKERKSFGKPISEHQAIAFKLADMATQIEAARLLVYKAAWL 305 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSAALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 +D G P SMAKL+AS++A V A+Q GGYG++ ++ +ER+ RD ++ QIYEGT Sbjct: 306 KDQGLPYTQAGSMAKLYASKVAMDVTIEAVQVHGGYGFVKEYHVERLMRDAKITQIYEGT 365 Query: 364 SDIQRMVISRNL 375 S+IQ+MVISR + Sbjct: 366 SEIQKMVISREV 377 Lambda K H 0.319 0.134 0.387 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: 340 Number of extensions: 15 Number of successful extensions: 2 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: 379 Length adjustment: 30 Effective length of query: 345 Effective length of database: 349 Effective search space: 120405 Effective search space used: 120405 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