Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_028316890.1 G491_RS0128020 acyl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000429905.1:WP_028316890.1 Length = 381 Score = 332 bits (852), Expect = 8e-96 Identities = 170/372 (45%), Positives = 240/372 (64%) Query: 4 TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63 TE+ ++R R F E L P A + D+E RFP E +++M LG+FG+ VP+ GG Sbjct: 6 TEKHREVRRSVRAFCEAELAPIAKDLDQEARFPWEVVEKMGALGYFGIQVPKDLGGAGMD 65 Query: 64 YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 ++Y + +EEI+ G ++VHNSV PI+ FG EQ+ K++ LA+G +GAF L Sbjct: 66 SVSYVVAIEEISRVCGGMGLCVTVHNSVAVHPIMAFGTREQQVKWVPDLAAGKKIGAFCL 125 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP AGSDAS ++ A +GDHYV+N K F+T+G A ++F T+P AG RGIS + Sbjct: 126 TEPNAGSDASGIQAVALKDGDHYVVNANKVFVTNGGVADTCLIFVRTNPEAGPRGISVIV 185 Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVG 243 +PG+ V +ED G + I D ++P + LG+EG G I LA L+ GR+G Sbjct: 186 AERGTPGFVVGDLEDLCGMRCNPVSSIRLNDCRIPEDHLLGKEGIGLAIGLAGLDTGRIG 245 Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IAAQA+G+A+AA E Y+++R F PI +HQ+VA +ADMATQ+ AR MV+ AAAL Sbjct: 246 IAAQALGIAQAALEEGIRYSKQRRQFKVPIAKHQSVANMIADMATQVDAARLMVYRAAAL 305 Query: 304 RDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGT 363 +D +P E++MAKLFA+E A V MA+Q GGYGY D+P+ER +RD RV +IYEGT Sbjct: 306 KDLKKPFSKESAMAKLFAAETASTVTDMAVQIHGGYGYSKDYPVERYFRDARVTRIYEGT 365 Query: 364 SDIQRMVISRNL 375 S++ R VI+R++ Sbjct: 366 SEVHRTVIARSV 377 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: 358 Number of extensions: 12 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: 381 Length adjustment: 30 Effective length of query: 345 Effective length of database: 351 Effective search space: 121095 Effective search space used: 121095 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