Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate Ga0059261_2860 Ga0059261_2860 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Korea:Ga0059261_2860 Length = 372 Score = 270 bits (691), Expect = 4e-77 Identities = 153/377 (40%), Positives = 215/377 (57%), Gaps = 8/377 (2%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 MDF + Q++L ++V+ L Y+ +R K + G ++ +W + AE GL+G F E Sbjct: 1 MDFHYDDNQQMLHDTVDRFLTDKYNLVTRHKLLGDLEGQAQ-LWREMAELGLIGAAFPEG 59 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 GG+GA V+ ++VME G LV PYL T ++ G L G + + +I G Sbjct: 60 VGGYGASPVDALVVMERFGRHLVTLPYLMTAIVCGRLLIAGG----RTDMIERVIAGDAR 115 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 A A + S TA +G GW I G VV+ G++ADT IV ART G DR Sbjct: 116 LALAAGSTHVLRSAEHHSFTAAAAGAGWTIRGRMPVVIGGDSADTFIVAARTSGALGDRD 175 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 G+ +FLV AD + R+ + D AA++ + VG DA + + + L+E +D Sbjct: 176 GITLFLVDADQ--VARRSFRMIDAHGAAEVVIDALSVGEDAVLSEIGGGVALVELALDHG 233 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 A C EA+G M + T EY +TR+Q+G P+ FQVLQHR ADM++ TE ARSMA A Sbjct: 234 IAAACGEAIGSMGHLVPATAEYTRTREQYGAPLAKFQVLQHRMADMYIQTETARSMAYVA 293 Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360 +M+ D ERA ++AAKVQIGKSGKFVG Q++QLHGG+G++ E IGH++ RL + Sbjct: 294 SMSLG-DTPVERARIVSAAKVQIGKSGKFVGYQAVQLHGGMGVSEELDIGHHYIRLNTLN 352 Query: 361 QTFGDTDHHLARVSAGG 377 Q FGD HL R +A G Sbjct: 353 QMFGDPAFHLRRFAAAG 369 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: 384 Number of extensions: 16 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: 372 Length adjustment: 30 Effective length of query: 350 Effective length of database: 342 Effective search space: 119700 Effective search space used: 119700 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