Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate GFF1710 PGA1_c17340 acyl-CoA dehydrogenase AcdA
Query= reanno::ANA3:7025618 (385 letters) >FitnessBrowser__Phaeo:GFF1710 Length = 381 Score = 407 bits (1046), Expect = e-118 Identities = 196/380 (51%), Positives = 269/380 (70%) Query: 1 MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60 MDF E+Q D+A F + +APFA +W+ E PK + + GELGF +LY E G Sbjct: 1 MDFALTEEQTAIFDMAFAFGQEHIAPFARQWEAEGTIPKSLWPQIGELGFGALYVSEETG 60 Query: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120 G GLSRLDA+++FE LS C + A L+IHNM M+ ++ +D ++ + + + + Sbjct: 61 GAGLSRLDATLVFEALSMACPSVAAFLSIHNMCAKMLDSFASDEMKARIMPDILSMKTVL 120 Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGIS 180 SYCLTEPG+GSDAA+L+T+A + + Y ++G+K FISG G ++ V M R+G+ GPKG+S Sbjct: 121 SYCLTEPGSGSDAAALKTRAAKTNEGYTLNGTKAFISGGGYSDAYVCMVRSGEDGPKGVS 180 Query: 181 AIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGG 240 + + + G+ +G E+KMGW +QPT V FD+ ++P ANL+GEEG+GFT+AMKGLDGG Sbjct: 181 TVYVEDGTAGLSFGGLEEKMGWKSQPTAQVQFDDCKIPAANLVGEEGKGFTYAMKGLDGG 240 Query: 241 RINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLA 300 R+NIA+CS+G AQ AL QYM+ER+ FGK + FQ LQF+LADM EL AAR +R A Sbjct: 241 RLNIASCSLGAAQQALTMTLQYMSERKAFGKSIDQFQGLQFRLADMEIELQAARVFLRQA 300 Query: 301 AFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQI 360 A+KLD G P+A+ +CAMAK+F T+ G +V D LQ+HGGYGY+ +Y +E+ RD+RVHQI Sbjct: 301 AWKLDQGAPDASKHCAMAKKFVTEAGSKVVDQCLQLHGGYGYLADYGIEKLVRDLRVHQI 360 Query: 361 LEGTNEIMRLIIARRLLDEN 380 LEGTNEIMR+I AR LL EN Sbjct: 361 LEGTNEIMRVITARHLLAEN 380 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: 384 Number of extensions: 14 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 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