Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 3607889 Dshi_1297 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= reanno::Phaeo:GFF1011 (386 letters) >FitnessBrowser__Dino:3607889 Length = 387 Score = 648 bits (1671), Expect = 0.0 Identities = 319/386 (82%), Positives = 346/386 (89%) Query: 1 MFNASMTFDLGEDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITV 60 MF ASM FDLGE+V ALR+MVHRWAQERV+P+A E D+ N FP LW EMGELGLLGITV Sbjct: 1 MFMASMKFDLGEEVEALREMVHRWAQERVKPLAAETDRSNAFPNALWPEMGELGLLGITV 60 Query: 61 PEEFGGAGMSYLAHTVAVEEIARASASVSLSYGAHSNLCVNQIKLNGNAEQKAKYLPRLV 120 E +GGAGM YLAHTVAVEEI+RASAS+ LSYGAHSNLCVNQIKLNG QK KYLP+LV Sbjct: 61 DEAYGGAGMGYLAHTVAVEEISRASASIGLSYGAHSNLCVNQIKLNGTDAQKEKYLPKLV 120 Query: 121 SGEHVGALAMSEAGAGSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPD 180 SG HVGALAMSEAGAGSDVV M LRAEKRNDHYRLNG KYWITNGPDADTLVVYAKTDP+ Sbjct: 121 SGAHVGALAMSEAGAGSDVVGMKLRAEKRNDHYRLNGTKYWITNGPDADTLVVYAKTDPE 180 Query: 181 AGSKGMTAFLIEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVL 240 AGSKG+TAFLIEKE GFSTS HFDKLGMRGSNTAEL+FEDVEVPFENVLGEEG+GV VL Sbjct: 181 AGSKGITAFLIEKEMAGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVAVL 240 Query: 241 MSGLDYERVVLAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTA 300 MSGLDYERVVL+G+ GIMA C+DE+MPYM ER+QFG+PIGNFQLMQGKIADMYTAMN+A Sbjct: 241 MSGLDYERVVLSGVNIGIMAGCLDEVMPYMTERRQFGEPIGNFQLMQGKIADMYTAMNSA 300 Query: 301 RAYVYEVAKACDKGTVTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRD 360 RAY YEVAKACD+G VTRQDAAAC LYASE M AHQAVQA GGAG+L+D+PV R+FRD Sbjct: 301 RAYAYEVAKACDRGEVTRQDAAACVLYASEEGMKVAHQAVQAMGGAGFLNDSPVARMFRD 360 Query: 361 AKLMEIGAGTSEIRRMLIGRELMSQM 386 AKLMEIGAGTSEIRRML+GRELM+ M Sbjct: 361 AKLMEIGAGTSEIRRMLVGRELMAAM 386 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: 598 Number of extensions: 19 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: 387 Length adjustment: 30 Effective length of query: 356 Effective length of database: 357 Effective search space: 127092 Effective search space used: 127092 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