Align Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) (characterized)
to candidate WP_090447885.1 BLS63_RS21710 acyl-CoA dehydrogenase
Query= reanno::ANA3:7025618 (385 letters) >NCBI__GCF_900100495.1:WP_090447885.1 Length = 387 Score = 508 bits (1308), Expect = e-148 Identities = 240/379 (63%), Positives = 303/379 (79%) Query: 1 MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60 MDF +++QR D AR FA ELAP A WD EHHFP +V+++AGE G+ +LY E +G Sbjct: 1 MDFELSDEQRLLVDSARAFARHELAPHAGDWDREHHFPLEVLRRAGEQGYLALYLAEEDG 60 Query: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTDTLRQAWSEPLTTGQMLA 120 G+GLSRL A++IFE+L+ GC ATTA +TIHNMATWM+ ++ L+ W L +G++LA Sbjct: 61 GLGLSRLSAALIFEQLAAGCVATTAFMTIHNMATWMLASFADQALKDQWLPGLVSGELLA 120 Query: 121 SYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGIS 180 SYCLTEP AGSDAA L+T+A R+GD+Y++ GSK FISGAGSTE+L+VM RTG+ G KGIS Sbjct: 121 SYCLTEPDAGSDAAHLRTRAKRQGDDYLIDGSKCFISGAGSTEVLIVMARTGEDGAKGIS 180 Query: 181 AIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGG 240 +PAD+EG+ YG+ E KMGW AQPTR ++F+ VR+P N +G EGQGF +AMKGLDGG Sbjct: 181 CFLVPADAEGVKYGRNELKMGWCAQPTRSISFEGVRIPAGNRIGPEGQGFVYAMKGLDGG 240 Query: 241 RINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLA 300 R+NIA+CS+G AQAALE++ +Y+ ER+QFGKPL+ FQALQFKLADM T+L A+RQMVRLA Sbjct: 241 RLNIASCSLGAAQAALEQSLRYVEERKQFGKPLSEFQALQFKLADMLTDLTASRQMVRLA 300 Query: 301 AFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQI 360 A KLD EA+ YCAMAKRFATD F +C+ ALQ+HGGYGY+ +YPLER RD RVHQI Sbjct: 301 AHKLDQRHAEASLYCAMAKRFATDHCFNLCNEALQLHGGYGYLNDYPLERWVRDSRVHQI 360 Query: 361 LEGTNEIMRLIIARRLLDE 379 LEGTNEIMR+I+ARRLL++ Sbjct: 361 LEGTNEIMRVIVARRLLEQ 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: 451 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: 387 Length adjustment: 30 Effective length of query: 355 Effective length of database: 357 Effective search space: 126735 Effective search space used: 126735 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