Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate Ga0059261_3793 Ga0059261_3793 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Korea:Ga0059261_3793 Length = 381 Score = 123 bits (308), Expect = 1e-32 Identities = 99/298 (33%), Positives = 137/298 (45%), Gaps = 10/298 (3%) Query: 51 GLLGLPFSEEDGGFGAGAVETMIVMEALGHSLVL--EPYLPTVVIGGGFLRRAGSAAQKA 108 GL GL +EE GG G +E V +G + + V IG L AG++ QKA Sbjct: 48 GLFGLSIAEEFGGLGLTMLEECRVAIEMGRTTPAFRSTFGTNVGIGSQGLVMAGTSEQKA 107 Query: 109 AHLPGIIDGSKTFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIV 168 A LP I G +FA E + D G V A + GD + + G K + N + A V Sbjct: 108 AWLPRIASGEIITSFALTEPDVGSDSGAVKARAVRDGDVYRLSGTKRFITNADKASLFTV 167 Query: 169 TARTKGGQRDRTGVGVFLVPADAKGITRKGYPT----QDGLHAADITFTGVQVGADAAIG 224 ART G + GV FLVP D GI+ G P Q G AD+ F V V A +G Sbjct: 168 MART-GDEPGARGVSAFLVPRDLPGISI-GEPEKKMGQKGAKVADVIFDDVPVPAANRLG 225 Query: 225 DPENALELIEAVVDDARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAA 284 + ++ V+D R + A +VG+ + + V Y RKQFG PI Q++Q A Sbjct: 226 EEGEGFKIAMRVLDRGRLHISAVSVGVAERLIADCVAYASERKQFGKPIAEHQLIQAMLA 285 Query: 285 DMFVATEQARSMAMFATMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIG 342 D TE + A+ AA D K+ AAAK+ + V +++Q+ GG G Sbjct: 286 DS--KTECLAARALVLETAAAKDAGKDVVMESAAAKLFATEMVGRVADRAVQILGGAG 341 Lambda K H 0.318 0.135 0.388 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: 311 Number of extensions: 22 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: 380 Length of database: 381 Length adjustment: 30 Effective length of query: 350 Effective length of database: 351 Effective search space: 122850 Effective search space used: 122850 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