Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF3369 PGA1_c34220 acyl-CoA dehydrogenase AcdA
Query= BRENDA::P26440 (426 letters) >FitnessBrowser__Phaeo:GFF3369 Length = 387 Score = 216 bits (550), Expect = 1e-60 Identities = 138/380 (36%), Positives = 198/380 (52%), Gaps = 8/380 (2%) Query: 44 GLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEF--KNLREFWKQLGNLGVLGITAPVQY 101 GLSEEQ + T F+ + L P E++RS + +RE + G+ P + Sbjct: 4 GLSEEQSMIVDTTRAFVTKELYPHELEVERSGHLPMELVREIQAKAIEAGLYAANMPEEV 63 Query: 102 GGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEY 161 GG+GL L +L +E+ RA+ A+ + A + ++ G E QKEKYL I GE Sbjct: 64 GGAGLDTLTWLLYEKELGRANYALHWTCVARPS----NILLAGTEEQKEKYLYPCIRGEK 119 Query: 162 IGALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPA 221 LAM+EP AGSD+ M A + G+ +ILNG K +I++ AD IV+ T P Sbjct: 120 WDCLAMTEPGAGSDLRGMTATARQDGDEFILNGTKHFISHADIADFAIVFMATGEEDTPR 179 Query: 222 S--RGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVL 279 + ITAF V+KG PGF+ + RG L F+DC++P +++LG +KG V Sbjct: 180 GPKKKITAFFVDKGTPGFTIRDGYRNVSHRGYTNAVLEFDDCRLPKSSVLGEVDKGFDVA 239 Query: 280 MSGLDLERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMAC 339 + L RL +A LG + LDH I Y R FGQ+IG FQ + K+ADM T L A Sbjct: 240 NTWLGATRLQVAATCLGRAERALDHAISYAAERRQFGQQIGKFQGVSFKLADMATELKAA 299 Query: 340 RQYVYNVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRD 399 + A D+G T D + L + E VA + IQ GG G +++ P+ R RD Sbjct: 300 NLLTWEAAWKFDQGSVTEADMSMAKLKATEMLAMVADEAIQIHGGMGLMDELPLERIWRD 359 Query: 400 AKLYEIGAGTSEVRRLVIGR 419 A++ I GTSE++R +I R Sbjct: 360 ARVERIWEGTSEIQRHIISR 379 Lambda K H 0.321 0.137 0.410 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: 423 Number of extensions: 21 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: 426 Length of database: 387 Length adjustment: 31 Effective length of query: 395 Effective length of database: 356 Effective search space: 140620 Effective search space used: 140620 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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