Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate GFF1029 HP15_1008 acyl-CoA dehydrogenase domain protein
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__Marino:GFF1029 Length = 383 Score = 261 bits (667), Expect = 2e-74 Identities = 149/379 (39%), Positives = 212/379 (55%), Gaps = 4/379 (1%) Query: 1 MLLTQDQE---MIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEF 57 M ++ D+E M RD+V + E+ PH W+K P++ L G + VPEE+ Sbjct: 1 MTVSVDKEELAMFRDSVIKVLEKEVTPHYEAWEKSGLVPRELWNTLGNAGMLCVDVPEEW 60 Query: 58 GGANLDYLTLALVLEEIAA-GDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGE 116 GG + +V EE+A G G ST + V + V L GN +Q++ WL L GE Sbjct: 61 GGIGAPFQFSVVVGEELARMGFGALSTNVMVHSDIVAPYLSHMGNEEQRQQWLPKLVSGE 120 Query: 117 MLGAFCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTDKGAGK 176 +GA +TEP GSD A+RT+AVK GDEY++NG K FIT+G++ + IV A TD AG Sbjct: 121 AVGAIAMTEPGAGSDLQAIRTSAVKDGDEYILNGSKTFITNGQHADMVIVAAKTDPKAGA 180 Query: 177 KGMSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGA 236 +G+S FLV T+ PG+ R DK+GQHS DT+++ F + RIPA L+G EG+G+ + Sbjct: 181 RGISLFLVDTSLPGFSKGRNLDKIGQHSGDTSELFFSDMRIPASALLGEEGQGFVYLMKE 240 Query: 237 LEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAARQL 296 L R+ I A V AR + D +AY++ERE FG + Q F +A T + Sbjct: 241 LPRERLVIGALGVAAARGSLDLTIAYAQERELFGQKLAQLQNTRFEIARMETDYRVNKAF 300 Query: 297 IWHAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRV 356 + D G+ A+MAK A+EM RV +Q GGYG ++P+ R + D RV Sbjct: 301 VDQCIDQYDLGELDAPTASMAKYSATEMQCRVADGCLQLFGGYGYTTEYPISRAFIDARV 360 Query: 357 CQIYEGTSDVQKIIIQRAL 375 +IY GTS+V K II R++ Sbjct: 361 QRIYGGTSEVMKEIIARSV 379 Lambda K H 0.319 0.134 0.396 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: 348 Number of extensions: 9 Number of successful extensions: 2 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: 376 Length of database: 383 Length adjustment: 30 Effective length of query: 346 Effective length of database: 353 Effective search space: 122138 Effective search space used: 122138 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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