Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Echvi_1212 Echvi_1212 Acyl-CoA dehydrogenases
Query= reanno::Phaeo:GFF1011 (386 letters) >FitnessBrowser__Cola:Echvi_1212 Length = 379 Score = 286 bits (732), Expect = 7e-82 Identities = 155/378 (41%), Positives = 228/378 (60%) Query: 6 MTFDLGEDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFG 65 M F L E+ A+++ +A+ + P E D FP E ++MGELG LG+ V ++ Sbjct: 1 MNFTLTEEHLAVQEAAREFAKSALLPGVIERDTHATFPHEQVKQMGELGFLGMMVAPQYN 60 Query: 66 GAGMSYLAHTVAVEEIARASASVSLSYGAHSNLCVNQIKLNGNAEQKAKYLPRLVSGEHV 125 G GM L++ +A+EEI++ AS +++ +++L ++ G+ +QK KYL L +GE + Sbjct: 61 GGGMDTLSYVLAIEEISKIDASAAVAMSVNNSLVCWGLEHYGSEQQKEKYLKPLAAGEIL 120 Query: 126 GALAMSEAGAGSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPDAGSKG 185 GA +SE AGSD S AEK DHY LNG K WITNG A +V A+T+P+ KG Sbjct: 121 GAFCLSEPEAGSDATSQRTMAEKHGDHYLLNGTKNWITNGGTASVYLVMAQTNPELKHKG 180 Query: 186 MTAFLIEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGLD 245 ++ F++EK+ +GF + DKLG+RGS+T L+F DV+VP EN +GE+G G M LD Sbjct: 181 ISTFIVEKDMEGFQVGKKEDKLGIRGSDTHSLMFNDVKVPLENRIGEDGFGFTYAMHSLD 240 Query: 246 YERVVLAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYVY 305 R+ +A GI A + + Y KERK FG+PI Q +Q K+ADM T + AR V+ Sbjct: 241 GGRIGIAAQALGIAAGAYELALAYSKERKAFGKPISQHQAIQFKLADMATEIEAARMLVW 300 Query: 306 EVAKACDKGTVTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDAKLME 365 + A D+G +A LYAS+VAM +AVQ GG G++ + V R+ RDAK+ + Sbjct: 301 KAAWLKDQGESYAHASAMAKLYASKVAMDTTIEAVQIHGGYGFVKEYHVERLMRDAKITQ 360 Query: 366 IGAGTSEIRRMLIGRELM 383 I GTSEI++++I R L+ Sbjct: 361 IYEGTSEIQKIVISRNLL 378 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: 364 Number of extensions: 22 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: 386 Length of database: 379 Length adjustment: 30 Effective length of query: 356 Effective length of database: 349 Effective search space: 124244 Effective search space used: 124244 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 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