Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_011840308.1 RSPH17029_RS01585 acyl-CoA dehydrogenase family protein
Query= reanno::Smeli:SM_b21121 (387 letters) >NCBI__GCF_000015985.1:WP_011840308.1 Length = 555 Score = 228 bits (580), Expect = 4e-64 Identities = 147/385 (38%), Positives = 204/385 (52%), Gaps = 14/385 (3%) Query: 10 LGEEIDALRASVRRFASERIAPLADDAD-RSNAFPMSLWREMGELGLLGITADEAHGGAG 68 L EE++ +R RRFA ER+AP A R PM + + E+G+ G+T E GG G Sbjct: 171 LDEELEMIRDQFRRFADERVAPHAHGWHMRDELIPMEIVEALAEMGVFGLTIPEEFGGFG 230 Query: 69 LGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVGAL 128 L + V EE+SR VG S G S + I G AQK+ +LPKL SGE + Sbjct: 231 LSKASMVVVSEELSRGYIGVG-SLGTRSEIAAELILCGGTDAQKAAWLPKLASGEILPTA 289 Query: 129 AMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGP-RGIT 187 +EP GSD+ S++ +A K GD +V+NG+K WIT+ V+ + A+TDP RG++ Sbjct: 290 VFTEPNTGSDLGSLRTRAVKDGDEWVVNGNKTWITHAARTHVMTLLARTDPETTDYRGLS 349 Query: 188 AFLVEKAFPGFSA---------GQKLDKLGMRGSNTSELIFTDCEVPEENVLGGV-GEGV 237 FL EK PG A G +++ LG RG E+ F V EN+LGGV G+G Sbjct: 350 MFLAEK-MPGTDADPFPTPGMTGGEIEVLGYRGMKEYEIGFDGFRVKGENLLGGVEGQGF 408 Query: 238 KVLMSGLDYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTM 297 K LM + R+ +A +G+ L+V + Y ERKQFG+ + EF + GKLA M V + Sbjct: 409 KQLMQTFESARIQTAARAIGVAQNALEVGMQYAEERKQFGKALIEFPRVAGKLAMMAVEI 468 Query: 298 NAARAYVYAVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRL 357 AR Y A D G+ +A L A A A A A+Q GGNG+ +Y R+ Sbjct: 469 MVARQLTYHSAWEKDHGQRCDLEAGMAKLLGARVAWAAADNALQIHGGNGFALEYQISRI 528 Query: 358 LRDAKLYEIGAGTSEIRRMLIGREL 382 L DA++ I G +EI+ +I R L Sbjct: 529 LCDARILNIFEGAAEIQAQVIARRL 553 Lambda K H 0.318 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: 421 Number of extensions: 26 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: 387 Length of database: 555 Length adjustment: 33 Effective length of query: 354 Effective length of database: 522 Effective search space: 184788 Effective search space used: 184788 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. 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