Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate BPHYT_RS06720 BPHYT_RS06720 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__BFirm:BPHYT_RS06720 Length = 375 Score = 260 bits (665), Expect = 4e-74 Identities = 156/381 (40%), Positives = 213/381 (55%), Gaps = 11/381 (2%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 MDF ++EQ+ +++ L SY F++R+ + + G S A W F+E GL LP E Sbjct: 1 MDFTFNDEQQQFADALRRYLDKSYGFEARQATVRSETGVSDAHWAAFSELGLTALPVPEA 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGS-AAQKAAHLPGIIDGSK 119 GGF G ++ ++VM+ LG +LV+EPY T V G LR AGS + A+ L G Sbjct: 61 QGGFNGGPIDMLVVMQELGRALVVEPYWATAV-GIEALRLAGSDQGEDASLLERAAQGEI 119 Query: 120 TFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDR 179 A A E ++R+DL V T+A G+ + G+K VV +G AD IV AR G Sbjct: 120 KLAMAFHEPHARYDLFAVETSANGQGEQLTLTGKKSVVQHGAQADYWIVPARLNGE---- 175 Query: 180 TGVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDD 239 + +F+V +A G+ Y T DG AA + F A G A L E + D Sbjct: 176 --IALFVVARNAAGVEITDYRTIDGQRAATLEFNNTP--ARRLAGKHAGAAAL-EHIADY 230 Query: 240 ARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMF 299 LCAEA+G +D TV+Y KTR+QFG PI FQ LQHR +M + EQARS+ Sbjct: 231 GTVLLCAEAIGALDALNLATVDYTKTRQQFGQPIARFQALQHRMVEMLIHAEQARSVTYL 290 Query: 300 ATMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMI 359 A M DA ER A++AAK ++G++ +FVGQQ++QLHGG+G+T E H FKRL +I Sbjct: 291 AAMRYTSMDADERRRAVSAAKARVGQAARFVGQQAVQLHGGMGVTNEVAAAHLFKRLAII 350 Query: 360 EQTFGDTDHHLARVSAGGGLI 380 E T GD DHHLAR +A G + Sbjct: 351 ETTLGDVDHHLARFAALPGFV 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: 327 Number of extensions: 16 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