Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate BPHYT_RS13555 BPHYT_RS13555 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__BFirm:BPHYT_RS13555 Length = 375 Score = 311 bits (798), Expect = 1e-89 Identities = 167/377 (44%), Positives = 235/377 (62%), Gaps = 3/377 (0%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 M+F +E++R+L +++ + Y F +R + A+ G+S +W +FAE G++G F E Sbjct: 1 MNFQHTEDRRMLADTLNRFVSEQYAFSTRDRIAQSDQGYSGELWSRFAELGIIGALFDEA 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 DGGFG G + +V E+LG LV+EP+L T+++G + R+G+ AQKA L +IDGS+ Sbjct: 61 DGGFGGGGFDIAVVFESLGRGLVVEPFLDTLIVGRA-IARSGNEAQKAV-LGELIDGSRI 118 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 A A E +S ++L VS A++SG W ++G K VV +GE A +V+ART G Sbjct: 119 VALAHGEPDSHYELSRVSARAERSGSTWQLNGAKAVVQHGEHASLFLVSARTGGDDDSDA 178 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 G+ +FLVP DA G++ +GY DG AA++T V + DA +G P+ +E + Sbjct: 179 GITLFLVPRDAAGVSVRGYRKIDGGRAAEVTLDNVTLSDDALLGTPDAGFATLEYAIGCG 238 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 ALC+EAVG MD + T+EY++TRKQFGVPIGSFQ LQHR AD+ + EQARS A+ Sbjct: 239 VFALCSEAVGAMDVAKDYTLEYLRTRKQFGVPIGSFQALQHRMADLLLEIEQARS-AVIN 297 Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360 AA + K R A++AAK IG+ G V ++ IQLHGGIGMT E + HY KRL MI+ Sbjct: 298 AAAALGAERKVRERAVSAAKYSIGRIGALVAEECIQLHGGIGMTWELPLAHYAKRLVMID 357 Query: 361 QTFGDTDHHLARVSAGG 377 GD DHHL R A G Sbjct: 358 HQLGDEDHHLERFVALG 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: 426 Number of extensions: 19 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: 375 Length adjustment: 30 Effective length of query: 350 Effective length of database: 345 Effective search space: 120750 Effective search space used: 120750 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