Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_108358862.1 B9Z44_RS01325 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF1051 (387 letters) >NCBI__GCF_003063475.1:WP_108358862.1 Length = 387 Score = 251 bits (642), Expect = 2e-71 Identities = 140/382 (36%), Positives = 213/382 (55%), Gaps = 8/382 (2%) Query: 12 ETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGAGLGY 71 E+ D+L +Q F+ + P +++ + PAD+ EMGL G+++ EE+GG GL Sbjct: 6 ESFDLLLPTLQRFIQERLVPAENYLEEHDEVPADIVEDMKEMGLFGLSIPEEFGGIGLSM 65 Query: 72 LAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGALAMS 131 V EI R S + +G + + I +G PEQKA LPK+ SGE + + A++ Sbjct: 66 SQEVQVAYEIGRTSLAFRSVFGTNVGIGSQGILMDGTPEQKANILPKVASGELIMSFALT 125 Query: 132 EPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGITAFIV 191 EP+AGSD S+K RA+ GD YVLNG+K +ITN P A + + A+T GA G+++FIV Sbjct: 126 EPDAGSDAASLKTRADLDGDHYVLNGTKRYITNAPRAGAFTLMARTG-GPGAGGVSSFIV 184 Query: 192 ERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENG-GVKVLMSGLDYERVV 250 D G G K+G RG+ TC++ ++V VP N++G G G K M LD R+ Sbjct: 185 PSDLPGIKLGKTDKKMGQRGTKTCDVILENVRVPAANIIGGVPGQGFKTAMKVLDRGRLH 244 Query: 251 LAGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYAVAQA 310 ++ G+ ++ Y DRKQFG++IGEFQ IQ +AD +L A + + VAQ Sbjct: 245 ISAVSCGMAHRIIEEATAYARDRKQFGKAIGEFQLIQAMLADSQAELLAGWSLVQDVAQR 304 Query: 311 CDRGETTRKD------AAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLY 364 D D + L+ E ++A + +Q+ GG GYINE+P R RD +L Sbjct: 305 FDGKPAHVSDPDVSMRVSCAKLFCTEMVGRVADRGVQVHGGAGYINEYPVERFYRDVRLL 364 Query: 365 EIGAGTSEIRRMLIGRELFNES 386 + GT++I++++IGREL ++ Sbjct: 365 RLYEGTTQIQQLIIGRELLRQA 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: 389 Number of extensions: 16 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: 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