Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__azobra:AZOBR_RS20220 Length = 382 Score = 283 bits (724), Expect = 6e-81 Identities = 178/390 (45%), Positives = 235/390 (60%), Gaps = 38/390 (9%) Query: 19 GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNRNVARMATLLAGLP 78 G L+ VR DDL A + L+ R ++ + I+DV++GCA GE N+AR + LA LP Sbjct: 24 GELAKVRPDDLLAHVVAALVERTG-VNPQDIEDVVVGCAFPEGEQGMNIARTVSFLAKLP 82 Query: 79 QSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPFVMGKAASAFSRQA 138 + TTINR CGS + A+ AA AI+ G G++ + GG+ESMSR P +MG Sbjct: 83 LTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIESMSRVP-MMG---------- 131 Query: 139 EMFDTTIGWRFVNPLMAQQFGTDSMPE-------TAENVAELLKISREDQDSFALRSQQR 191 NPL D PE TAENVA +ISR DQ++ A S + Sbjct: 132 -----------YNPLPHPGL-KDHYPEAYCSMGVTAENVARRYEISRADQEAMAAESHAK 179 Query: 192 TAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPFRANGVITAG 251 A AQ +G LAEEIV + + G+V + D +RP T+ E L GLK F A+G +TAG Sbjct: 180 AAAAQQAGRLAEEIVAI--QTAAGLV---ERDGCIRPGTSGETLSGLKPAFLADGSVTAG 234 Query: 252 NASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPATRRVLERAG 311 +S + DGA+A+++ +E A A GL ARI ++A AG P +MGLGPVPA ++ L RAG Sbjct: 235 TSSPLTDGASAVLVTTEAYAKANGLPILARIRSVAVAGCAPEVMGLGPVPAAQKALARAG 294 Query: 312 LSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMSGARLALAAS 371 LSI D+DVIELNEAFAAQA+ +R+L + D VN +GGAIALGHPLG +GAR+ A+ Sbjct: 295 LSIRDIDVIELNEAFAAQAIACMRDLDI--DPAKVNLDGGAIALGHPLGATGARITGKAA 352 Query: 372 HELHRRNGRYALCTMCIGVGQGIAMILERV 401 L R ++AL T CIG GQGIA +LE V Sbjct: 353 ALLKREGKQFALATQCIGGGQGIATVLEAV 382 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: 435 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 401 Length of database: 382 Length adjustment: 31 Effective length of query: 370 Effective length of database: 351 Effective search space: 129870 Effective search space used: 129870 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