Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_004328657.1 C665_RS19360 acyl-CoA dehydrogenase
Query= reanno::Phaeo:GFF1011 (386 letters) >NCBI__GCF_000310185.1:WP_004328657.1 Length = 378 Score = 256 bits (653), Expect = 1e-72 Identities = 139/377 (36%), Positives = 212/377 (56%), Gaps = 2/377 (0%) Query: 6 MTFDLGEDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFG 65 M F L + +RD+ R+A+ + P A + D FP E+ Q ELGLLGI +PE G Sbjct: 1 MDFQLNPEQREIRDLARRFAEREIAPRAAQADLDKAFPTEVHQRAQELGLLGINLPETVG 60 Query: 66 GAGMSYLAHTVAVEEIARASASVSLSYGAHSNLCVNQIKLNGNAEQKAKYLPRLVSGEHV 125 G G+ L + E R + + ++ L I + G Q+++YL G + Sbjct: 61 GGGLGCLELVLVTEAFCRGCLGIGTALCVNA-LATEPIVIAGTDAQRSRYLGAAARGA-L 118 Query: 126 GALAMSEAGAGSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPDAGSKG 185 + AM+E GAGSDV + RAE+ YRL G+K WI+N A+ VV+AKT PD G +G Sbjct: 119 ASFAMTEPGAGSDVAGIRTRAERVEGGYRLTGSKIWISNANLAEFFVVFAKTAPDGGHRG 178 Query: 186 MTAFLIEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGLD 245 M+AF++ + G + + KLG R S T E+ + V VP ++ LGEEG G + M+ D Sbjct: 179 MSAFIVPRASAGLTVGEPLGKLGQRCSPTCEVFLDQVFVPEDHRLGEEGGGFALAMAVFD 238 Query: 246 YERVVLAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYVY 305 + R ++A G G++ C+DE + Y +R G+ + + Q + K+A+M + AR Y Sbjct: 239 HSRPMVAAFGVGLIERCLDESLAYATQRSSMGKRLIDHQAVAHKLAEMRMRLEAARLLTY 298 Query: 306 EVAKACDKGTVTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDAKLME 365 + A D+G +A+ +A++ AM A +AVQ FGG GY ++ PV ++FRDAK+++ Sbjct: 299 QSAWLLDQGRPNTIEASIAKAFAADAAMWAATEAVQIFGGMGYSTEYPVEKLFRDAKVLQ 358 Query: 366 IGAGTSEIRRMLIGREL 382 I GTSEI+R +I REL Sbjct: 359 IYEGTSEIQRNIIAREL 375 Lambda K H 0.318 0.132 0.382 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: 386 Number of extensions: 20 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: 386 Length of database: 378 Length adjustment: 30 Effective length of query: 356 Effective length of database: 348 Effective search space: 123888 Effective search space used: 123888 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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