Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_012332335.1 M446_RS11800 acyl-CoA dehydrogenase
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_000019365.1:WP_012332335.1 Length = 380 Score = 460 bits (1184), Expect = e-134 Identities = 229/375 (61%), Positives = 279/375 (74%) Query: 3 FNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGM 62 F EDQ D+AR FAA+ +AP A WD E HFP +V+++AG LG + E GG Sbjct: 4 FTLPEDQIAIRDMARSFAAERIAPHALAWDAEKHFPVEVLREAGALGMGGITIREEHGGS 63 Query: 63 GLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLASY 122 GL+RLDA++IFE L+ GC +A L+IHNMATWM+ +G++ R+ W L + LA+Y Sbjct: 64 GLTRLDAALIFEALATGCPTVSAFLSIHNMATWMIDRFGSEPQRERWLPDLCRAERLAAY 123 Query: 123 CLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGISAI 182 CLTEPG+GSDAA+L+T A REGD YV+ G+K FISGAG+ +L VVM RTG+ GPKGIS + Sbjct: 124 CLTEPGSGSDAAALRTTARREGDAYVLDGTKQFISGAGAVDLYVVMVRTGEPGPKGISTL 183 Query: 183 AIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGGRI 242 +PAD+ G+ +G E KMGWNAQPTR V F RVP AN LGEEG GF AM GLDGGRI Sbjct: 184 VVPADAPGLSFGPNERKMGWNAQPTRQVIFSGCRVPAANRLGEEGIGFKIAMAGLDGGRI 243 Query: 243 NIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLAAF 302 NI CS+G AQ+AL++A Y ER+ FG+ L AFQALQF+LADMATEL AAR M+ AA Sbjct: 244 NIGACSLGGAQSALDKALTYARERRAFGQRLDAFQALQFRLADMATELEAARLMIYAAAA 303 Query: 303 KLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQILE 362 LD GDP+ATA AMAKRFATD GFQV DAALQ+HGGYGY+ EY +E+ RD+RVHQILE Sbjct: 304 ALDRGDPDATARAAMAKRFATDRGFQVADAALQLHGGYGYLSEYGIEKIVRDLRVHQILE 363 Query: 363 GTNEIMRLIIARRLL 377 GTNEIMRLI+AR L+ Sbjct: 364 GTNEIMRLIVARGLV 378 Lambda K H 0.320 0.134 0.396 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: 450 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: 385 Length of database: 380 Length adjustment: 30 Effective length of query: 355 Effective length of database: 350 Effective search space: 124250 Effective search space used: 124250 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