Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_011951498.1 SWIT_RS03310 acyl-CoA dehydrogenase
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_000016765.1:WP_011951498.1 Length = 381 Score = 441 bits (1134), Expect = e-128 Identities = 209/375 (55%), Positives = 276/375 (73%) Query: 3 FNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGM 62 F EDQR ++AR+F AD + P AA+WDE+H FP++ IQ A LGF +Y E GG+ Sbjct: 5 FELTEDQRAIQEMARKFTADAITPHAAEWDEKHIFPRETIQAAAALGFGGIYVSEEAGGI 64 Query: 63 GLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLASY 122 GL RL+A++I E ++ GC +T+A ++IHNMA WM+ +G+D L+ + + + + SY Sbjct: 65 GLGRLEAALIMEAMAYGCPSTSAFISIHNMAAWMIDRFGSDDLKGRYLPDMIACRRMGSY 124 Query: 123 CLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGISAI 182 CLTEPG+GSDAA+L+T+AVR+GD+YVVSGSK FISG G E+ VVM RTG+ GPKGIS + Sbjct: 125 CLTEPGSGSDAAALKTRAVRDGDDYVVSGSKAFISGGGENEVYVVMVRTGEDGPKGISCL 184 Query: 183 AIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGGRI 242 I D G+ +G E K+GW++QPT V FD VRVPVAN +G EG+GF AM GLDGGR+ Sbjct: 185 VIDKDMPGVSFGAQEKKLGWHSQPTAQVNFDGVRVPVANRVGGEGEGFRIAMMGLDGGRL 244 Query: 243 NIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLAAF 302 NI CS+G AQ L+ + Y ER+QFG+P+A FQ++QF LADM TEL AAR ++ AA Sbjct: 245 NIGACSLGGAQRCLDESVSYTRERKQFGQPIADFQSIQFTLADMETELQAARMLLYAAAA 304 Query: 303 KLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQILE 362 K+ + P+ T + AMAKRFATD G V D ALQ+HGGYGY+R+YP+ER +RD+RVH+ILE Sbjct: 305 KVTANAPDKTRFAAMAKRFATDTGSAVVDRALQLHGGYGYLRDYPIERFWRDLRVHRILE 364 Query: 363 GTNEIMRLIIARRLL 377 GTNEIMR+I +R LL Sbjct: 365 GTNEIMRMITSRELL 379 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: 403 Number of extensions: 16 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: 381 Length adjustment: 30 Effective length of query: 355 Effective length of database: 351 Effective search space: 124605 Effective search space used: 124605 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