Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF1710 PGA1_c17340 acyl-CoA dehydrogenase AcdA
Query= reanno::Phaeo:GFF1011 (386 letters) >FitnessBrowser__Phaeo:GFF1710 Length = 381 Score = 223 bits (567), Expect = 9e-63 Identities = 128/384 (33%), Positives = 207/384 (53%), Gaps = 9/384 (2%) Query: 6 MTFDLGEDVNALRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFG 65 M F L E+ A+ DM + QE + P A++ + + P LW ++GELG + V EE G Sbjct: 1 MDFALTEEQTAIFDMAFAFGQEHIAPFARQWEAEGTIPKSLWPQIGELGFGALYVSEETG 60 Query: 66 GAGMSYLAHTVAVEEIARASASVSLSYGAHSNLCVNQIKLNGNAEQKAKYLPRLVSGEHV 125 GAG+S L T+ E ++ A SV+ H N+C + + E KA+ +P ++S + V Sbjct: 61 GAGLSRLDATLVFEALSMACPSVAAFLSIH-NMCAKMLDSFASDEMKARIMPDILSMKTV 119 Query: 126 GALAMSEAGAGSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPDAGSKG 185 + ++E G+GSD ++ RA K N+ Y LNG K +I+ G +D V ++ D G KG Sbjct: 120 LSYCLTEPGSGSDAAALKTRAAKTNEGYTLNGTKAFISGGGYSDAYVCMVRSGED-GPKG 178 Query: 186 MTAFLIEKEFKGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGLD 245 ++ +E G S +K+G + TA++ F+D ++P N++GEEGKG M GLD Sbjct: 179 VSTVYVEDGTAGLSFGGLEEKMGWKSQPTAQVQFDDCKIPAANLVGEEGKGFTYAMKGLD 238 Query: 246 YERVVLAGIGTGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYVY 305 R+ +A G + + YM ERK FG+ I FQ +Q ++ADM + AR ++ Sbjct: 239 GGRLNIASCSLGAAQQALTMTLQYMSERKAFGKSIDQFQGLQFRLADMEIELQAARVFLR 298 Query: 306 EVAKACDKGTVTRQDAAACCL----YASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDA 361 + A D+G DA+ C + +E Q +Q GG GYL+D + ++ RD Sbjct: 299 QAAWKLDQGA---PDASKHCAMAKKFVTEAGSKVVDQCLQLHGGYGYLADYGIEKLVRDL 355 Query: 362 KLMEIGAGTSEIRRMLIGRELMSQ 385 ++ +I GT+EI R++ R L+++ Sbjct: 356 RVHQILEGTNEIMRVITARHLLAE 379 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: 361 Number of extensions: 18 Number of successful extensions: 4 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: 381 Length adjustment: 30 Effective length of query: 356 Effective length of database: 351 Effective search space: 124956 Effective search space used: 124956 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