Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_043745120.1 AMB_RS18150 acyl-CoA dehydrogenase
Query= BRENDA::B5UB85 (416 letters) >NCBI__GCF_000009985.1:WP_043745120.1 Length = 378 Score = 239 bits (610), Expect = 1e-67 Identities = 141/380 (37%), Positives = 208/380 (54%), Gaps = 7/380 (1%) Query: 33 FGLSEEQQQLRKMVFDFAQKELAPKAAEIDKENNFKELRPFWKKLGDLGLLGITASSDYG 92 FGL+ +Q+ R+ DFA E+AP AA D+E F E +K +LG GI D G Sbjct: 3 FGLTPDQEAFRQAAHDFAVGEMAPHAAHWDEEGIFPE--DTLRKAAELGFAGIYVGEDVG 60 Query: 93 GTGGKYSDHCVIMEELSRASGGIALSYGAHSNLCVNQINRNGTEEQKSKYLPKLCSGEHI 152 G+ D +I EEL+ A A H N+ I+ G +EQ+ ++LP LCS Sbjct: 61 GSALSRLDAALIFEELAAACPSTAAYISIH-NMAAWMIDSFGDQEQRRRFLPDLCSMRKF 119 Query: 153 GALAMSEPGSGSDVVSMKLRAEKKGDYYVLNGNKFWITNGPDADVLVVYAKTNWSTSKQQ 212 + ++EP +GSD S++ +AE+ GD+YVLNG K +I+ G +DV VV +T K Sbjct: 120 ASYCLTEPNAGSDAASLRTKAERDGDHYVLNGTKAFISGGGRSDVYVVMVRTGAPGPK-- 177 Query: 213 HGISAFLIEKDYPGFSTAQKLDKLGMRGSNTGELVFEDCKVPAANLLGQENKGVYVLMSG 272 GIS ++E PG S ++ KLG + T ++FEDC+VP AN +G E G + M G Sbjct: 178 -GISCLVVEAGTPGLSFGKQEKKLGWKTQPTASVIFEDCRVPVANRIGAEGDGFKIAMKG 236 Query: 273 LDLERLVLAAGPVGLMQAAIDTAFLYAHTRKQFGKNIGEFQLIQGKMADMYTTLSACRSY 332 LD R+ + A +G +A ++ A Y R+QFG+ I FQ Q K+ADM T L A R Sbjct: 237 LDGGRINIGACSLGGARACLEHAIEYTGQRQQFGQAISAFQATQFKLADMATELEAARLM 296 Query: 333 LYNVAKACDNGHVNSK-DCAGVILYCAEKATQVALDAIQILGGNGYINDYPTGRILRDAK 391 ++ A + D+ + CA + V A+Q+ GG GYI +YP R RD + Sbjct: 297 IHRAAHSLDSKSPQATVHCAMAKRMATDVGFAVTDAALQLHGGYGYIKEYPIERYFRDLR 356 Query: 392 LYEIGAGTSEVRRMLIGRAL 411 +++I G++E+ R++IGRAL Sbjct: 357 VHQILEGSNEIMRVIIGRAL 376 Lambda K H 0.318 0.135 0.399 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: 394 Number of extensions: 20 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: 416 Length of database: 378 Length adjustment: 31 Effective length of query: 385 Effective length of database: 347 Effective search space: 133595 Effective search space used: 133595 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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