Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate Ga0059261_3681 Ga0059261_3681 Acyl-CoA dehydrogenases
Query= reanno::ANA3:7025618 (385 letters) >FitnessBrowser__Korea:Ga0059261_3681 Length = 380 Score = 445 bits (1144), Expect = e-129 Identities = 211/374 (56%), Positives = 276/374 (73%) Query: 3 FNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGM 62 F+ NEDQR ++AR+F AD + P AA+WDE+H FP++ ++ A ELGF ++Y E GG+ Sbjct: 4 FDLNEDQRAIQEMARKFTADAITPHAAEWDEKHIFPRETVKAAAELGFGAIYVSEESGGI 63 Query: 63 GLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLASY 122 GL RL++++I E ++ GC AT+A ++IHNMA+WM+ +G+ ++ + L T LASY Sbjct: 64 GLGRLESALIMEAMAYGCPATSAFISIHNMASWMIDRFGSQAVKDKYLPRLVTADWLASY 123 Query: 123 CLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGISAI 182 CLTEP +GSDAA+L+T A R+GD ++V+GSK FISGAG EL V M RTG GPKGIS + Sbjct: 124 CLTEPSSGSDAAALKTTAKRDGDHFIVNGSKQFISGAGENELYVTMVRTGADGPKGISCL 183 Query: 183 AIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGGRI 242 AI D G+ +G E K+GW+AQPTR VTFDNVRVPV NL+G EG+GF AM GLDGGR+ Sbjct: 184 AIEKDMPGVSFGANERKLGWHAQPTRQVTFDNVRVPVENLVGGEGEGFRIAMMGLDGGRL 243 Query: 243 NIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLAAF 302 NI CS+G AQ L+ A QY +R+QFG +A FQ QF LADMATEL AAR ++ LAA Sbjct: 244 NIGACSLGGAQRCLDEAVQYTKDRKQFGSAIADFQNTQFMLADMATELEAARALLYLAAA 303 Query: 303 KLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQILE 362 K+ S P+ T + AMAKRFATD G V D ALQ+HGGYGY+ +YP+ER +RD+RVH ILE Sbjct: 304 KVTSNAPDKTKFAAMAKRFATDTGSSVVDRALQLHGGYGYLMDYPIERFWRDLRVHSILE 363 Query: 363 GTNEIMRLIIARRL 376 GTN++MR+I+ R L Sbjct: 364 GTNQVMRMIVGREL 377 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: 385 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: 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 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