Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_010628345.1 BZY95_RS09135 acyl-CoA dehydrogenase
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_002151265.1:WP_010628345.1 Length = 389 Score = 540 bits (1392), Expect = e-158 Identities = 264/387 (68%), Positives = 312/387 (80%), Gaps = 2/387 (0%) Query: 1 MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60 M+F+ +DQR A F+ ELA AA+WD HFP DVI++AGE GF +Y PE G Sbjct: 1 MEFSLTDDQRALVQAAADFSQAELADHAAEWDATSHFPVDVIRRAGEAGFLGIYIPEERG 60 Query: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120 G+GLSRLDAS+IFE+LS+GC ATTA LTIHNM WMV +WG+D LR+ W E L +G+ L Sbjct: 61 GLGLSRLDASLIFEQLSQGCIATTAYLTIHNMVAWMVASWGSDELRETWVERLISGECLG 120 Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTG--QAGPKG 178 YCLTEPG+GSDAASL+TKAVREGDEYV+SGSKMFISGAG+ ++LVVM RTG +G G Sbjct: 121 CYCLTEPGSGSDAASLRTKAVREGDEYVISGSKMFISGAGANDMLVVMARTGAPDSGAGG 180 Query: 179 ISAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLD 238 +SAI +PAD+ GI YGK E+KMGW +QPTRL++FD VRVPV NLLGEEGQGF AMKGLD Sbjct: 181 VSAILVPADAAGIEYGKNEEKMGWKSQPTRLISFDGVRVPVGNLLGEEGQGFKLAMKGLD 240 Query: 239 GGRINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVR 298 GGR+NIA+CS+G AQ AL A Y+ ER+QFG+ LA FQALQFKLADMATEL AAR MVR Sbjct: 241 GGRLNIASCSLGAAQHALTLARNYLQERKQFGRELAHFQALQFKLADMATELTAARLMVR 300 Query: 299 LAAFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVH 358 AA++LD GDPEATAYCAMAKRFATD+GF VC+ ALQ+HGGYGY+RE+PLER RD RVH Sbjct: 301 HAAWRLDQGDPEATAYCAMAKRFATDMGFNVCNEALQLHGGYGYLREFPLERMVRDTRVH 360 Query: 359 QILEGTNEIMRLIIARRLLDENAGQIL 385 QILEGTNEIMR+I+ARRLL + + L Sbjct: 361 QILEGTNEIMRVIVARRLLTDGTIEAL 387 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: 500 Number of extensions: 16 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: 385 Length of database: 389 Length adjustment: 30 Effective length of query: 355 Effective length of database: 359 Effective search space: 127445 Effective search space used: 127445 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