Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate BPHYT_RS25385 BPHYT_RS25385 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__BFirm:BPHYT_RS25385 Length = 384 Score = 276 bits (705), Expect = 9e-79 Identities = 155/375 (41%), Positives = 213/375 (56%), Gaps = 4/375 (1%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 M+F LS EQ+LL++SV + Y F++R + K + S W FA+ G L E Sbjct: 1 MNFTLSAEQQLLQDSVRRFVDRDYSFETRMAFVKARSTCSATHWQTFADNGWLAAALPES 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 GGF +T+++ LG LV+EPYL V+ L + AQ+ LP + DGS+ Sbjct: 61 CGGFDGSLTDTVLIASELGRGLVIEPYLGCAVLAAQTLLAGATPAQREQWLPALADGSRK 120 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 FA A E SR V T+A + DG+ + G K +VL G AD+ IV+AR + D Sbjct: 121 FALAYSEAQSRGFPEFVETSATPTPDGYSLAGSKTLVLGGADADSFIVSARAQ----DAE 176 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 G+ + LVP DA G+ R+ P DG AA++T GV+V +A +G P L + + A Sbjct: 177 GITLMLVPGDAPGLARRVLPLHDGSFAAELTLDGVRVTREAVLGVPGPGLTALRHALSHA 236 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 AL AE VG M++S+ T EY++ RKQFGVPIGSFQ LQHR ADM E ARSM Sbjct: 237 TAALGAELVGAMEKSIELTAEYLRVRKQFGVPIGSFQALQHRLADMAAEMELARSMLHAL 296 Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360 + E D R A++ AK IG++ +FV Q+IQLHGGIGMT E ++GHY+KR + + Sbjct: 297 LGSLENDAPPARLRAVSQAKSVIGRAARFVCGQAIQLHGGIGMTEEYQVGHYYKRAVVAD 356 Query: 361 QTFGDTDHHLARVSA 375 FG +D H A +A Sbjct: 357 ALFGSSDQHDAACAA 371 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: 362 Number of extensions: 20 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: 384 Length adjustment: 30 Effective length of query: 350 Effective length of database: 354 Effective search space: 123900 Effective search space used: 123900 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