Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate GFF3369 PGA1_c34220 acyl-CoA dehydrogenase AcdA
Query= reanno::MR1:200844 (385 letters) >FitnessBrowser__Phaeo:GFF3369 Length = 387 Score = 215 bits (547), Expect = 2e-60 Identities = 141/393 (35%), Positives = 202/393 (51%), Gaps = 17/393 (4%) Query: 1 MDFNFNEDQRQFAELARQFATDELAPFAAKWDEEHHFPKDVIQ----KAGELGFCSLYSP 56 M F +E+Q + R F T EL P + + H P ++++ KA E G + P Sbjct: 1 MQFGLSEEQSMIVDTTRAFVTKELYPHELEVERSGHLPMELVREIQAKAIEAGLYAANMP 60 Query: 57 ESEGGMGLSRLDASIIFEELSKGCTAT--TAMLTIHNMATWMVTTWGTETLRQAWSEPLT 114 E GG GL L + +EL + A T + N + GTE ++ + P Sbjct: 61 EEVGGAGLDTLTWLLYEKELGRANYALHWTCVARPSN-----ILLAGTEEQKEKYLYPCI 115 Query: 115 TGQMLASYCLTEPGAGSDAASLQTKAVPDGDEYVVSGSKMFISGAGSTELLVVMCRTGQA 174 G+ +TEPGAGSD + A DGDE++++G+K FIS A + +V TG+ Sbjct: 116 RGEKWDCLAMTEPGAGSDLRGMTATARQDGDEFILNGTKHFISHADIADFAIVFMATGEE 175 Query: 175 ----GPKG-ISAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQG 229 GPK I+A + + G + ++ FD+ R+P +++LGE +G Sbjct: 176 DTPRGPKKKITAFFVDKGTPGFTIRDGYRNVSHRGYTNAVLEFDDCRLPKSSVLGEVDKG 235 Query: 230 FTFAMKGLDGGRINIATCSVGTAQAALERASQYMNERQQFGKPLAAFQALQFKLADMATE 289 F A L R+ +A +G A+ AL+ A Y ER+QFG+ + FQ + FKLADMATE Sbjct: 236 FDVANTWLGATRLQVAATCLGRAERALDHAISYAAERRQFGQQIGKFQGVSFKLADMATE 295 Query: 290 LVAARQMVRLAAFKLDSGDPEGTAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLE 349 L AA + AA+K D G A +MAK AT++ V D A+QIHGG G + E PLE Sbjct: 296 LKAANLLTWEAAWKFDQGSVT-EADMSMAKLKATEMLAMVADEAIQIHGGMGLMDELPLE 354 Query: 350 RHFRDVRVHQILEGTNEIMRLIIARRLLDENAG 382 R +RD RV +I EGT+EI R II+R LL G Sbjct: 355 RIWRDARVERIWEGTSEIQRHIISRELLRAQGG 387 Lambda K H 0.319 0.134 0.396 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: 345 Number of extensions: 18 Number of successful extensions: 5 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: 385 Length of database: 387 Length adjustment: 30 Effective length of query: 355 Effective length of database: 357 Effective search space: 126735 Effective search space used: 126735 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