Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Ga0059261_4052 Ga0059261_4052 Acyl-CoA dehydrogenases
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__Korea:Ga0059261_4052 Length = 385 Score = 509 bits (1312), Expect = e-149 Identities = 262/378 (69%), Positives = 300/378 (79%), Gaps = 3/378 (0%) Query: 6 LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMS-LWREMGELGLLGITADEAH 64 ++FAL E + +R + +RFA ERI PLA D + FP LW MGELGL GIT DE Sbjct: 6 MDFALSETAEMIRDTTQRFAKERIEPLAAKIDAEDWFPRDELWTAMGELGLHGITVDEEF 65 Query: 65 GGAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEH 124 GG GLGYL H +A EE+SRASAS+GLSYGAHSNLCVNQI+R PAQK++YLP+LISGEH Sbjct: 66 GGLGLGYLEHVIACEEVSRASASIGLSYGAHSNLCVNQISRWASPAQKAKYLPRLISGEH 125 Query: 125 VGALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPR 184 VG+LAMSE GAGSDVVSMKL+A+ +GDRYVLNG+K WITN AD LVVYAKT G R Sbjct: 126 VGSLAMSEAGAGSDVVSMKLRAEHKGDRYVLNGTKFWITNAAYADTLVVYAKT--GEGSR 183 Query: 185 GITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGL 244 GIT FL+EK PGFS GQK+DK+GMRGS T+EL+F DCEVPEENV+G + GV VLMSGL Sbjct: 184 GITTFLIEKDMPGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENVMGPLNGGVGVLMSGL 243 Query: 245 DYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYV 304 DYER VL+ LGIM ACLDVV+PYL ERKQFGQ IG FQLMQ K+ADMYV +N+ARAYV Sbjct: 244 DYERTVLAGIQLGIMQACLDVVLPYLRERKQFGQAIGSFQLMQAKVADMYVALNSARAYV 303 Query: 305 YAVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLY 364 YAVA ACD G+T R DAAG IL A+E A +A EA+QALGG GYT D+P R LRDAKL Sbjct: 304 YAVAQACDAGKTTRFDAAGAILLASENAFRVAGEAVQALGGAGYTKDWPVERFLRDAKLL 363 Query: 365 EIGAGTSEIRRMLIGREL 382 +IGAGT+EIRRMLIGREL Sbjct: 364 DIGAGTNEIRRMLIGREL 381 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: 413 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: 387 Length of database: 385 Length adjustment: 30 Effective length of query: 357 Effective length of database: 355 Effective search space: 126735 Effective search space used: 126735 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