Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_043768478.1 U743_RS11515 isovaleryl-CoA dehydrogenase
Query= reanno::Smeli:SM_b21121 (387 letters) >NCBI__GCF_000733765.1:WP_043768478.1 Length = 387 Score = 584 bits (1505), Expect = e-171 Identities = 289/381 (75%), Positives = 319/381 (83%) Query: 6 LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHG 65 LN LG ++DALR + FA IAP+A+ D N FP LW ++GELG LG+TA E G Sbjct: 6 LNHDLGPDLDALREAAADFARREIAPIAESTDADNVFPRQLWPKLGELGALGMTAGEDVG 65 Query: 66 GAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHV 125 G G+GYLAH V MEEISRAS S+GLSYGAHSNLCVNQ+++NG P Q+ +YLPKLISGEHV Sbjct: 66 GMGMGYLAHVVLMEEISRASGSIGLSYGAHSNLCVNQLDKNGSPDQRQKYLPKLISGEHV 125 Query: 126 GALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRG 185 GALAMSEPGAGSDVVSMKL+ADK+GDRYVLNGSKMWITNGPDAD LVVYAKTDP AGPRG Sbjct: 126 GALAMSEPGAGSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADTLVVYAKTDPEAGPRG 185 Query: 186 ITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLD 245 ITAF+VEK GFS QKLDKLGMRGSNT EL+F +CEVPEENVLG VG+GV VLMSGLD Sbjct: 186 ITAFIVEKGMAGFSTAQKLDKLGMRGSNTCELVFDNCEVPEENVLGAVGKGVNVLMSGLD 245 Query: 246 YERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVY 305 YERVVLS GP+G+M A LD+V PY+HER+QFG PIG FQLMQGKLADMYV + R+YVY Sbjct: 246 YERVVLSGGPVGLMQAALDIVTPYVHERQQFGDPIGSFQLMQGKLADMYVGTSVCRSYVY 305 Query: 306 AVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYE 365 AVA ACDRGET RKDAAG ILYAAEKAT +AIQALGGNGY N+Y GRL RDAKLYE Sbjct: 306 AVARACDRGETTRKDAAGAILYAAEKATWACGQAIQALGGNGYINEYATGRLWRDAKLYE 365 Query: 366 IGAGTSEIRRMLIGRELFAET 386 IGAGTSEIRRMLIGRELF ET Sbjct: 366 IGAGTSEIRRMLIGRELFDET 386 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: 469 Number of extensions: 14 Number of successful extensions: 1 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: 387 Length adjustment: 30 Effective length of query: 357 Effective length of database: 357 Effective search space: 127449 Effective search space used: 127449 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 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