Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate WP_015819506.1 TERTU_RS08405 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >NCBI__GCF_000023025.1:WP_015819506.1 Length = 594 Score = 124 bits (312), Expect = 5e-33 Identities = 112/376 (29%), Positives = 165/376 (43%), Gaps = 49/376 (13%) Query: 37 KDAHQGLAALGAYGICVPEEFGGANLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAIL 96 K+A+Q G I ++GG L ++ E A + S +++ +N L Sbjct: 80 KEAYQQFVEGGWPSINHSVDYGGQGLPESVGTIISEMTGAANWAWSMYPGLSHGAMNT-L 138 Query: 97 MRYGNAQQKRDWLTPLARGEMLGAFCLTEPHVGSDASALRTTAVKQGD-EYVINGVKQFI 155 ++G +QK +LT L G G CLTE H G+D L+T A Q D Y I G K FI Sbjct: 139 AQHGTVEQKSVYLTKLVEGSWTGTMCLTEAHCGTDLGMLKTRAEPQDDGSYRIQGSKIFI 198 Query: 156 TSGKNGQ----VAIVIA-VTDKGAGKKGMSAFLVPTNNP---GYVVAR-------LEDKL 200 ++G + V IV+A + D G KG+S F+VP P G V R +E K+ Sbjct: 199 SAGDHDLAENIVHIVLARLPDAPEGTKGISLFIVPKYLPAEDGSVGERNAVTCGSIEHKM 258 Query: 201 GQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALEGGRIGIAAQSVGMARSAFDAAL 260 G H + T +NFD+ LIG G + R+G A Q + A + +L Sbjct: 259 GIHGNATCVLNFDDA---TGYLIGPPNRGLHCMFTFMNTARLGTALQGLAHAEVGYQKSL 315 Query: 261 AYSKERESF------------GTAIFNHQAVGFRLADCATQIEAARQLIWHAAAL----- 303 +Y+KER I H V L E R LI + + L Sbjct: 316 SYAKERLQMRALSGPKNPSGPADPIIVHPDVRRMLLTQKAFAEGGRMLIHYCSQLVDIEQ 375 Query: 304 --RDAGKPCLKEAA--------MAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRD 353 DAG+ EAA +AK F +E + A+Q GG+G + ++ VE+ RD Sbjct: 376 LSDDAGRKT--EAADLLAFLTPIAKAFLTETGFEAANHALQCFGGHGYIREWGVEQNVRD 433 Query: 354 VRVCQIYEGTSDVQKI 369 R+ +YEGT+ +Q + Sbjct: 434 ARIAMLYEGTTGIQAL 449 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: 489 Number of extensions: 23 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: 376 Length of database: 594 Length adjustment: 33 Effective length of query: 343 Effective length of database: 561 Effective search space: 192423 Effective search space used: 192423 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: 51 (24.3 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