Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Echvi_2990 Echvi_2990 Acyl-CoA dehydrogenases
Query= reanno::ANA3:7024494 (389 letters) >FitnessBrowser__Cola:Echvi_2990 Length = 402 Score = 221 bits (564), Expect = 2e-62 Identities = 126/367 (34%), Positives = 206/367 (56%), Gaps = 5/367 (1%) Query: 18 MLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPEEYGGANMGYLAHV 77 ++R +++DF K E++P + D FP+EI P G +G G +P +YGG + Y+++ Sbjct: 34 LIRQSLRDFVKKEVSPYIEEWAQDAHFPSEIVPKFGEIGAFGPQIPAKYGGGGLDYISYG 93 Query: 78 VAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSGEHIGALAMSEPNA 137 + M+EI R + + + +L + I+ G+ EQ+ K+LPKL SGE +G ++EP+ Sbjct: 94 LIMQEIERGDSGMRSTVSVQGSLVMYPIHAFGSEEQREKFLPKLASGEWLGCFGLTEPDH 153 Query: 138 GSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKGAHGITAFIVERGF 197 GS+ + + GD Y+LNG KMWI+N P+A+ V++AK D HG+ IVERG Sbjct: 154 GSNPGGLTTSFKDNGDHYLLNGAKMWISNAPEADIAVVWAK-DENGRIHGL---IVERGM 209 Query: 198 KGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMSGLDYERVVLSGGP 257 +GF+ K +R S T ELVF++V+VP+EN+L G +G+ + LD R ++ G Sbjct: 210 EGFTTPTTHHKWSLRASCTGELVFDNVKVPKENLLPG-KSGLSAPLMCLDAARYGIAWGA 268 Query: 258 LGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKAYVYSVAKSCDRGE 317 +G C + Y ER QF K I FQLVQ KLA+M T + A+ + + D+G+ Sbjct: 269 IGAAMDCYESAKRYAMERIQFDKPIAAFQLVQKKLAEMLTEITKAQLLAWRLGTLKDQGK 328 Query: 318 TTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAGTSEIRR 377 T + A + +A ++A +A Q+ GG G +Y R + + + GT +I Sbjct: 329 ATSAQISMAKRNNVAMALEIAREARQIHGGMGITGDYPIMRHMMNLESVITYEGTHDIHL 388 Query: 378 MLIGREL 384 +++G+E+ Sbjct: 389 LILGQEI 395 Lambda K H 0.316 0.135 0.388 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: 380 Number of extensions: 14 Number of successful extensions: 3 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: 389 Length of database: 402 Length adjustment: 31 Effective length of query: 358 Effective length of database: 371 Effective search space: 132818 Effective search space used: 132818 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 (21.6 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