Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_01875 CCNA_01875 acyl-CoA dehydrogenase, short-chain specific
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Caulo:CCNA_01875 Length = 381 Score = 129 bits (323), Expect = 2e-34 Identities = 103/316 (32%), Positives = 143/316 (45%), Gaps = 21/316 (6%) Query: 51 GLLGLPFSEEDGGFGAGAVETMIVMEALGHSLVL--EPYLPTVVIGGGFLRRAGSAAQKA 108 GL GL E GG G E V+ A H+ + V IG L G AQKA Sbjct: 47 GLFGLSIPESYGGLGLSLEEEARVIVAFCHTAPAFRSTFGTNVGIGSQGLVMFGDEAQKA 106 Query: 109 AHLPGIIDGSKTFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIV 168 LP I G AFA E + D V T A + GD +V++G K + N A+ V Sbjct: 107 RWLPSIASGETITAFALTEAEAGSDSASVQTRAVRDGDHYVLNGVKRYITNAGRANLFTV 166 Query: 169 TARTKGGQRDRTGVGVFLVPADAKGITRKGYPT----QDGLHAADITFTGVQVGADAAIG 224 ART + GV FLVPAD G++ G P Q G H D+ F V+V + +G Sbjct: 167 MARTDPNTKGGAGVSAFLVPADLPGLS-VGKPEKKMGQQGAHIHDVVFEDVRVPVENRLG 225 Query: 225 DPENALELIEAVVDDARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAA 284 + V+D R + A VG+ + + V Y RKQFG PI SFQ++Q A Sbjct: 226 AEGEGFTVAMRVLDRGRVHISAVCVGVAERLIADCVAYASERKQFGQPIASFQLIQAMIA 285 Query: 285 DMFVATEQARSMAMFATMAAEFDDAKER-AGA-----IAAAKVQIGKSGKFVGQQSIQLH 338 D +++ A+ A A FD A++R AGA AA K+ + V +++Q+ Sbjct: 286 D-------SKTEAL-AAKALVFDTARKRDAGANVTLEAAATKLFASEMVGRVADRAVQVF 337 Query: 339 GGIGMTMEAKIGHYFK 354 GG G + I ++ Sbjct: 338 GGAGYVADYGIERLYR 353 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: 324 Number of extensions: 19 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: 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