Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS36650 RR42_RS36650 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Cup4G11:RR42_RS36650 Length = 375 Score = 311 bits (796), Expect = 2e-89 Identities = 165/372 (44%), Positives = 223/372 (59%), Gaps = 4/372 (1%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 MDF+ SEEQ++L +S+ + Y FD R+K A+ G +RA W + AE G+LGL E Sbjct: 1 MDFNYSEEQQMLADSLRRFIDTEYTFDKRRKSARGGGSLNRATWAQLAEMGVLGLTVPGE 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 GGFG A ++V LG LVLEP PT V+ L GS AQK LP I G + Sbjct: 61 YGGFGESAASQLVVQRELGRGLVLEPVTPTAVMATAVLSAYGSDAQKNDWLPAIAAGERV 120 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 A LE +R+ +A++ GDG+V++G K + +GEAAD ++TAR G Sbjct: 121 VTLAYLEPTTRYRPETARASAERKGDGYVLNGNKSLAWHGEAADAFLLTARVCGSNE--- 177 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 + +FLVP +A G+T GYPT D L AAD+ V V A A IG+ + L + +D Sbjct: 178 -LALFLVPGNAAGLTVHGYPTMDSLRAADLALQNVIVDASAMIGNAADGLPALLHGIDHG 236 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 ALCAEA G M++ + T EY++TR+QFG P+ FQ LQHR ADM V E A SMA A Sbjct: 237 IAALCAEAAGAMEKLIEITAEYLRTRQQFGKPLAVFQALQHRMADMLVQKELALSMAYVA 296 Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360 A + D +R ++AAKV + K+G+ VGQQ++QLHGG+GMT E ++G YFKRLTMI+ Sbjct: 297 AQALDETDPAQRRRMLSAAKVTVAKAGRLVGQQAVQLHGGMGMTDELEVGDYFKRLTMID 356 Query: 361 QTFGDTDHHLAR 372 GD+D H+ R Sbjct: 357 PLLGDSDFHVQR 368 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: 366 Number of extensions: 14 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: 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