Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate BPHYT_RS09180 BPHYT_RS09180 3-ketoacyl-CoA thiolase
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__BFirm:BPHYT_RS09180 Length = 394 Score = 321 bits (822), Expect = 3e-92 Identities = 184/404 (45%), Positives = 248/404 (61%), Gaps = 16/404 (3%) Query: 2 REAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61 R+ + G+RT IG +GG+L DL A +RE+L R + + + V+ G Sbjct: 3 RDVVVVSGVRTAIGGFGGSLKDFSPTDLGARVVREVLAR-ANVSGDEVGHVVFGNVVHTE 61 Query: 62 EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121 + +AR+A + G+ Q T+NRLCGSGL A+ AA+++ GD D+ I GG E+MS Sbjct: 62 PKDMYLARVAAINGGVAQHAPALTVNRLCGSGLQAIVSAAQSVLLGDADIAIGGGAENMS 121 Query: 122 RAPFVMGKAASAFSRQ---AEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISR 178 RAP+ M A+ F ++ A + D +G + F + M TAENVA ISR Sbjct: 122 RAPYSM--PAARFGQRMGDARLVDMMVG------ALNDPFQSIHMGVTAENVARKYDISR 173 Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238 E QD+ AL S +R A A +SG E+I+P+ + +KKG V DEH R + E L Sbjct: 174 EAQDALALESHRRAANAITSGYFKEQILPITIPSKKGDVV-FDTDEHTRMSASPEDFSKL 232 Query: 239 KAPF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGL 297 K F + NG +TAGNASG+ND AAA+++ +A +G+ P AR+V+ A AGV+P MG+ Sbjct: 233 KPVFAKENGTVTAGNASGINDAAAAVVLMERSLAEQRGIKPLARLVSYAHAGVDPAYMGI 292 Query: 298 GPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGH 357 GPVPATRR LERAGL++ D+DVIE NEAFAAQA V +ELG D VNPNG I+LGH Sbjct: 293 GPVPATRRALERAGLTVADLDVIEANEAFAAQACAVSKELGF--DPAKVNPNGSGISLGH 350 Query: 358 PLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 P+G +GA + + A +EL R GRYAL TMCIG GQGIA I ER+ Sbjct: 351 PIGATGALITVKALYELQRIGGRYALVTMCIGGGQGIAAIFERI 394 Lambda K H 0.319 0.135 0.384 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: 420 Number of extensions: 19 Number of successful extensions: 6 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: 401 Length of database: 394 Length adjustment: 31 Effective length of query: 370 Effective length of database: 363 Effective search space: 134310 Effective search space used: 134310 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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