Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase
Query= reanno::MR1:200844 (385 letters) >NCBI__GCF_000192475.1:WP_010441027.1 Length = 385 Score = 227 bits (579), Expect = 4e-64 Identities = 131/374 (35%), Positives = 213/374 (56%), Gaps = 7/374 (1%) Query: 7 EDQRQFAELARQFATDELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGLSR 66 ++ R FAE+A +F D L P KW E+ +D +AG+ G + E GG+G Sbjct: 13 DEHRMFAEMAGRFMDDALVPNTEKWAEDGVVDRDFWLQAGQTGLMAGSIAEEYGGVGGGM 72 Query: 67 -LDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTETLRQAWSEPLTTGQMLASYCLT 125 D+ ++E+ ++G I ++ T +TT+G+E + W L +G+M+ + +T Sbjct: 73 GFDSVTLYEQTARGDAGWG--YGIQSIVTHYITTYGSEDQKHKWLPKLASGEMIGALAMT 130 Query: 126 EPGAGSDAASLQTKAVPDGDEYVVSGSKMFISGAGSTELLVVMCRTGQA-GPKGISAIAI 184 EPG GSD +++T A DG+ Y + GSK+FI+ S +L++V +T ++ G KG+S IA+ Sbjct: 131 EPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSLGAKGVSLIAV 190 Query: 185 PAD-SEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLG-EEGQGFTFAMKGLDGGRI 242 + +EG G+ +K+G T + F++V+VP+ NLLG EEGQGF MK L R+ Sbjct: 191 ETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQLMKQLPWERL 250 Query: 243 NIATCSVGTAQAALERASQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLAAF 302 I ++G A+ +Y+ ER+ FG+ + FQ +FKLA+ T+ R V Sbjct: 251 TIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLAECKTKAEVLRSFVNDCIG 310 Query: 303 KLDSGDPEGTAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQILE 362 KL++G+ + A +M K + ++V ++ LQ+ GGYG++ EYP+ R + D RV I Sbjct: 311 KLEAGELD-AATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEYPIARLYADARVQMIYG 369 Query: 363 GTNEIMRLIIARRL 376 GTNE+M+ +IAR L Sbjct: 370 GTNEVMKELIARSL 383 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: 370 Number of extensions: 21 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: 385 Length adjustment: 30 Effective length of query: 355 Effective length of database: 355 Effective search space: 126025 Effective search space used: 126025 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 24 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