Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate GFF403 PGA1_c04140 putative acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Phaeo:GFF403 Length = 381 Score = 243 bits (621), Expect = 5e-69 Identities = 144/376 (38%), Positives = 209/376 (55%), Gaps = 6/376 (1%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 M+F L+EE+++L++S+ L Y +R K + G+S A+W + A+ G+LG E Sbjct: 1 MNFQLTEERQMLQDSLRRFLADRYTVTARNKAIADPSGYSSAIWTQLADLGVLGALLPEA 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFL---RRAGSAAQKAAHLPGIIDG 117 GG+G + + E LG + V+EP L T V+ G L A + +L +I G Sbjct: 61 VGGYGGAGFDIATIFEELGRAGVVEPVLDTAVLCGSLLCGPHDAQPLPRDRQYLERLIAG 120 Query: 118 SKTFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQR 177 AFA E SR++ V TTA G V+ G K VV+N EAA+ LIV+AR G Sbjct: 121 DLQLAFAHGEPASRYERTWVETTATVGGQDIVLTGRKSVVVNAEAAELLIVSAREGGASG 180 Query: 178 DRTGVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVV 237 DR G+ +FLV G+ +G G A +I GV++ A +G A +E+ + Sbjct: 181 DRDGLSLFLVDPKTAGVRMQGSALLAGGRAGEIELDGVRLSPSARLGAAGGAAVRVESAL 240 Query: 238 DDARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMA 297 A AL AEA+G M+ + T++Y+ TR+QFG PIG+FQ LQHR A+M + EQARS Sbjct: 241 AAAEVALAAEALGAMETATRLTMDYLTTRQQFGRPIGTFQALQHRVAEMLIEVEQARSAV 300 Query: 298 MFATMAAEFDDAKE-RAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRL 356 + A A + A + R IAAA+ IG++G+ + +++IQLHGGI MT E ++ H KR+ Sbjct: 301 INA--AGHLEGAPQVRDRHIAAARNLIGRTGRHIAEEAIQLHGGIAMTAEYELAHIAKRI 358 Query: 357 TMIEQTFGDTDHHLAR 372 M E FGD D L R Sbjct: 359 VMSEHRFGDADTQLER 374 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: 343 Number of extensions: 15 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: 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