Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_011157692.1 TX73_RS10890 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2397 (379 letters) >NCBI__GCF_000195775.1:WP_011157692.1 Length = 379 Score = 266 bits (679), Expect = 9e-76 Identities = 147/374 (39%), Positives = 216/374 (57%), Gaps = 4/374 (1%) Query: 4 NEDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTG 63 N D A ++ R+F Q ++PFA +W +P E + AA+G G+ PE++GG+ Sbjct: 8 NADHIAFRDVIRRFVQNEIEPFATEWDEAGGFPRELYEKAAAIGLLGLGFPEEYGGTPCD 67 Query: 64 YLAYAMALEEIA-AGDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGAFA 122 + +A +E+A A G S ++ H S+G PI R G+ + K+ L + G++I A A Sbjct: 68 QFMWIVATQELARAAAGGVSASLNSH-SIGAPPIARAGSPELKARVLPEILSGKKISALA 126 Query: 123 LTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKGGISAF 182 +TEP GSD ++LRTRA RDGDHYV+NG K FITSG A I AV G GG+S Sbjct: 127 ITEPSGGSDVANLRTRAVRDGDHYVVNGEKTFITSGMRAD-YITTAVRTGGEGPGGVSLL 185 Query: 183 IVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRI 242 ++P D+PG ++ K+G ASDT + F++ RVP AN LG EG G+ I + N R+ Sbjct: 186 LIPGDTPGLTRTPLK-KMGWWASDTATLHFDNCRVPAANLLGTEGAGFMIIMMNFNSERL 244 Query: 243 GIAAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAA 302 +AA + ++ + A +YAR R TFGKP+++HQ + +L DMA +IA ++ M+ A Sbjct: 245 TMAAGCIAASKVCLDEATEYARQRVTFGKPLVKHQVIRHKLVDMAQKIAASQAMLELLAW 304 Query: 303 LREVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIYEG 362 + G + E M K A++ S A+Q GG GY+ VERIYRDV+V I G Sbjct: 305 RVDQGESPIAEICMLKNQATQTMAFCASEAVQIFGGAGYMRGVKVERIYRDVKVNAIGGG 364 Query: 363 TSDIQRLVISRNLG 376 T +I + + SR +G Sbjct: 365 TEEIMKDLASRQMG 378 Lambda K H 0.320 0.135 0.391 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: 377 Number of extensions: 12 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: 379 Length of database: 379 Length adjustment: 30 Effective length of query: 349 Effective length of database: 349 Effective search space: 121801 Effective search space used: 121801 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