Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate 3609216 Dshi_2602 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= reanno::MR1:200844 (385 letters) >FitnessBrowser__Dino:3609216 Length = 401 Score = 216 bits (551), Expect = 7e-61 Identities = 127/369 (34%), Positives = 201/369 (54%), Gaps = 4/369 (1%) Query: 16 ARQFATDELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGLSRLDASIIFEE 75 A AT+ +AP W+ +P+D KAG G LY+PE GG GL + ++E+ Sbjct: 12 AHTHATEVVAPNVDAWNAAKAWPRDASDKAGAAGLTGLYAPEDWGGQGLPLSEGIQVYEQ 71 Query: 76 LSKGCTATTAMLTIHNMATWMVTTWGTETLRQAWSEPLTTGQMLASYCLTEPGAGSDAAS 135 L G A L++HN+ T+ +GT+ ++ W+ LT G+ LA++ LTEP +GSD Sbjct: 72 LGLGDGAYAFALSMHNICTFAGCGYGTDAFKKKWARDLTAGRKLANFALTEPQSGSDPMK 131 Query: 136 LQTKAVPDGD-EYVVSGSKMFISGAGSTELLVVMCRTGQA-GPKGISAIAIPADSEGIIY 193 + T+A+ +GD + +SGSK ++S A ++ + +T A G K ++ IAIPAD+ GI + Sbjct: 132 MYTRAMINGDGTWTISGSKAWVSLATEADIYFTVVKTSDAPGHKDMAMIAIPADAPGISF 191 Query: 194 GKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGGRINIATCSVGTAQ 253 G + +N P + DNV V N++ GQG ++ +D R++IA+ G Q Sbjct: 192 GPLYETPSYNFLPMSEMYLDNVVVSEENIILPIGQGLQGSLMAIDIARVSIASGCCGLMQ 251 Query: 254 AALERASQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLAAFKLDSGDPEGTA 313 AAL+ A Y R+ FG +Q+ L ++AT+L A++ + R AA L G P+G Sbjct: 252 AALDTALSYSKSRKMFGGKNLDLDGIQWMLGEVATDLEASKLLYRRAAEAL--GTPDGPL 309 Query: 314 YCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQILEGTNEIMRLIIA 373 A AKRF D + + Q+ GG G ++ Y L+ R ++ +I++GT EI R++I Sbjct: 310 MAAHAKRFVPDAAVKAANTCTQVLGGMGLLQPYGLDGLSRLAQMLRIVDGTTEISRVVIG 369 Query: 374 RRLLDENAG 382 R L AG Sbjct: 370 RALQKRAAG 378 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: 362 Number of extensions: 16 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: 385 Length of database: 401 Length adjustment: 31 Effective length of query: 354 Effective length of database: 370 Effective search space: 130980 Effective search space used: 130980 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