Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate GFF814 PS417_04135 acyl-CoA dehydrogenase
Query= reanno::MR1:200844 (385 letters) >FitnessBrowser__WCS417:GFF814 Length = 378 Score = 263 bits (672), Expect = 6e-75 Identities = 152/375 (40%), Positives = 226/375 (60%), Gaps = 6/375 (1%) Query: 5 FNEDQRQFAELARQFATDELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGL 64 F+ + F E R F + APF W+++ + + + KAGE G + PE GG+G Sbjct: 7 FSPEHELFRESVRTFLEKDAAPFHGHWEKQGYIDRRLWNKAGEAGMLCSHLPEEYGGLGA 66 Query: 65 SRLDASIIFEELSK-GCTATTAMLTIHNMATWMVTTWGTETLRQAWSEPLTTGQMLASYC 123 L ++++ EE+S+ G T L +A +++ +G+E L+ + L +G+M+ + Sbjct: 67 DFLYSAVVIEEISRLGLTGIGFSLHSDIVAPYILH-YGSEALKHKYLPKLISGEMVTAIA 125 Query: 124 LTEPGAGSDAASLQTKAVPDGDEYVVSGSKMFISGAGSTELLVVMCRTG-QAGPKGISAI 182 +TEPGAGSD ++T AV DGDEYV++GSK FI+ EL++V+ +T +AG KG S Sbjct: 126 MTEPGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGYLAELVIVVAKTDPKAGAKGTSLF 185 Query: 183 AIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDGGRI 242 + AD+ G GK +K+G AQ T + F +VRVP NLLG+ G GF + M+ L R+ Sbjct: 186 LVEADTPGFDKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQERL 245 Query: 243 NIATCSVGTAQAALERASQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMV-RLAA 301 +A ++ +A+AALE +Y ER+ FGK +A FQ +FKLA+MATE+ R V + A Sbjct: 246 TVAIGALSSAEAALEWTLEYTRERKAFGKAIADFQNTRFKLAEMATEIQIGRVFVDKCMA 305 Query: 302 FKLDSGDPEGTAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQIL 361 L+ TA AMAK +ATD+ +V D +Q+HGGYG++ EYP+ R + D RV +I Sbjct: 306 LHLEGKLDVPTA--AMAKYWATDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIY 363 Query: 362 EGTNEIMRLIIARRL 376 GTNEIM+ IIAR L Sbjct: 364 AGTNEIMKEIIARAL 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: 348 Number of extensions: 13 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: 385 Length of database: 378 Length adjustment: 30 Effective length of query: 355 Effective length of database: 348 Effective search space: 123540 Effective search space used: 123540 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