Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate CA265_RS02820 CA265_RS02820 acyl-CoA dehydrogenase
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__Pedo557:CA265_RS02820 Length = 384 Score = 306 bits (784), Expect = 6e-88 Identities = 157/376 (41%), Positives = 231/376 (61%) Query: 7 NFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHGG 66 +F+ E +++A VR FA + I P + D + FP+ L++++GELGL+G+ E +GG Sbjct: 6 DFSETETQQSVKAMVRDFAEKNIRPHIMEWDEAQHFPVELFKQLGELGLMGVLVPEEYGG 65 Query: 67 AGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVG 126 +GLGY + + E++R S+GLS AH++LC I P QK R+LPKL + E +G Sbjct: 66 SGLGYQEYVDVIVEVARVCGSIGLSLAAHNSLCTGHILAFANPEQKQRWLPKLATAEWIG 125 Query: 127 ALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRGI 186 A ++E GSD + M A + GD Y++NG+K WIT+G D+ VV +T +GI Sbjct: 126 AWGLTEANTGSDALRMMTTAVEDGDDYIINGAKNWITHGKSGDIAVVMVRTGEQGSSKGI 185 Query: 187 TAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLDY 246 +A +VE+ PGF+AG+K +KLGMR S T+E+IF +C VP+ N+LG VGEG K M LD Sbjct: 186 SAIVVERGTPGFTAGKKENKLGMRASETTEMIFDNCRVPKANLLGNVGEGFKQAMKVLDG 245 Query: 247 ERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYA 306 R+ ++A LGI D V Y +R+QFGQPI FQ + KLADM + AA + Sbjct: 246 GRISIAALALGIAKGAFDAAVAYSKQRQQFGQPISSFQAISFKLADMATEIEAAELLIRQ 305 Query: 307 VAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYEI 366 A +R K++A +A+E + +A +A+Q GG GYT D+P + RD+KL I Sbjct: 306 AADLKNRHLPMTKESAMAKYFASEVSVRVATDAVQIFGGYGYTKDFPVEKFYRDSKLCTI 365 Query: 367 GAGTSEIRRMLIGREL 382 G GTSEI++++I RE+ Sbjct: 366 GEGTSEIQKIVIAREV 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: 291 Number of extensions: 9 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: 384 Length adjustment: 30 Effective length of query: 357 Effective length of database: 354 Effective search space: 126378 Effective search space used: 126378 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