Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate GFF3369 PGA1_c34220 acyl-CoA dehydrogenase AcdA
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Phaeo:GFF3369 Length = 387 Score = 253 bits (646), Expect = 6e-72 Identities = 149/382 (39%), Positives = 216/382 (56%), Gaps = 12/382 (3%) Query: 5 SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVE----KMAKAGMMGIPYPKEYGG 60 S++ M+ + +F E+ P E++ P E V K +AG+ P+E GG Sbjct: 6 SEEQSMIVDTTRAFVTKELYPHELEVERSGHLPMELVREIQAKAIEAGLYAANMPEEVGG 65 Query: 61 EGGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLG 120 G DT+ +++ +EL R A S I G EEQK+K+L P GEK Sbjct: 66 AGLDTLTWLLYEKELGRANYALHWTCVARPS----NILLAGTEEQKEKYLYPCIRGEKWD 121 Query: 121 AFGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMT---DKSKG- 176 +TEP AG+D G TA DGDE+ILNG+K FI++A D +V T D +G Sbjct: 122 CLAMTEPGAGSDLRGMTATARQDGDEFILNGTKHFISHADIADFAIVFMATGEEDTPRGP 181 Query: 177 NKGISAFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMS 236 K I+AF V+KGTPGF+ + + RG + L F+DCR+PK ++LG+ +GF +A + Sbjct: 182 KKKITAFFVDKGTPGFTIRDGYRNVSHRGYTNAVLEFDDCRLPKSSVLGEVDKGFDVANT 241 Query: 237 TLDGGRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARH 296 L R+ +AA LG A+ ALD + Y ER QFG+ + KFQ F+LADM +++AA Sbjct: 242 WLGATRLQVAATCLGRAERALDHAISYAAERRQFGQQIGKFQGVSFKLADMATELKAANL 301 Query: 297 LVYQAAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAK 356 L ++AA D G + +MAKL A E V +A+Q+HGG G + P+ER+ RDA+ Sbjct: 302 LTWEAAWKFDQGSVTEADMSMAKLKATEMLAMVADEAIQIHGGMGLMDELPLERIWRDAR 361 Query: 357 ITEIYEGTSEVQRMVISGKLLK 378 + I+EGTSE+QR +IS +LL+ Sbjct: 362 VERIWEGTSEIQRHIISRELLR 383 Lambda K H 0.315 0.133 0.373 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: 383 Number of extensions: 17 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: 378 Length of database: 387 Length adjustment: 30 Effective length of query: 348 Effective length of database: 357 Effective search space: 124236 Effective search space used: 124236 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: 42 (22.0 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