Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_011654402.1 RL_RS29285 acyl-CoA dehydrogenase
Query= reanno::Smeli:SM_b21121 (387 letters) >NCBI__GCF_000009265.1:WP_011654402.1 Length = 386 Score = 222 bits (566), Expect = 1e-62 Identities = 140/385 (36%), Positives = 204/385 (52%), Gaps = 13/385 (3%) Query: 6 LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMG----ELGLLGITAD 61 +NF L EE + + +VR F I P ++ +RS P L E+ +LG Sbjct: 1 MNFGLSEEQEMIVETVRAFVETEIYPHENEVERSGIVPPELGDEIRRKCIDLGFYACNFP 60 Query: 62 EAHGGAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLIS 121 E GGAGL ++ + E+ R S + + +G S + + + Q+ RYL + Sbjct: 61 EEVGGAGLDHVTFTLVERELGRGSLGLTVFFGRPSGILMAC-----EGEQRERYLLPAVR 115 Query: 122 GEHVGALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAA 181 GE + ALA++EP AGSD+ MK A + G +VLNG+K +I++ AD ++V+A T Sbjct: 116 GEKIDALAITEPDAGSDMRGMKCAARRDGSDFVLNGTKHFISHADVADFVIVFAATGEEE 175 Query: 182 GPRGI----TAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGV 237 P+GI TAFLV++ PGF + D + RG + S L FTDC +P VLG V G Sbjct: 176 TPKGIKKKITAFLVDRGTPGFEILKGYDSVSHRGYHNSTLSFTDCRIPGSQVLGEVHRGF 235 Query: 238 KVLMSGLDYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTM 297 ++ L R+ ++A +G D+ +PY ERKQFG+PIG Q + KLADM + Sbjct: 236 EIANQWLYGTRLTVAATCVGRARRVFDMTLPYAAERKQFGKPIGANQGVSFKLADMITEI 295 Query: 298 NAARAYVYAVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRL 357 +AA A A D G +A + A LY++E + EAIQ GG G +D P R Sbjct: 296 DAADWLTLAAAWRLDAGLSADRQIASAKLYSSEMLARVTDEAIQIFGGMGLMDDLPLARF 355 Query: 358 LRDAKLYEIGAGTSEIRRMLIGREL 382 RDA++ I GTSEI+R +I R+L Sbjct: 356 WRDARVERIWDGTSEIQRHIISRDL 380 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: 352 Number of extensions: 14 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: 386 Length adjustment: 30 Effective length of query: 357 Effective length of database: 356 Effective search space: 127092 Effective search space used: 127092 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