Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate YP_004140539.1 Mesci_1329 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000185905.1:YP_004140539.1 Length = 392 Score = 303 bits (777), Expect = 4e-87 Identities = 173/394 (43%), Positives = 241/394 (61%), Gaps = 10/394 (2%) Query: 6 ICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDNR 65 I RTP+G + GA ++ A +L A+ +RELL R E +D+VILG A + + Sbjct: 7 IASAARTPVGSFNGAFAATPAHELGAVVIRELLSRAGVEPGE-VDEVILGQVLTAAQ-GQ 64 Query: 66 NVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAPF 125 N AR A++ AGLP+ + +N++CGSGL A+ + I GD ++IAGG ESMS + Sbjct: 65 NPARQASINAGLPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQESMSLSTH 124 Query: 126 VMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQDSFA 185 A ++ DT I + F M TAENVA +I+REDQD FA Sbjct: 125 AQHLRAGVKMGDFKLIDTMI-----KDGLWDAFNGYHMGNTAENVARQFQITREDQDQFA 179 Query: 186 LRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPFRAN 245 L SQ + AQ +G +EIV V +K KKG T + DE++R T++ + LK F + Sbjct: 180 LASQNKAEAAQKAGKFKDEIVAVTIKGKKGD-TIVDQDEYIRHGATIDAMTKLKPAFDKD 238 Query: 246 GVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPATRR 305 G +TA NASG+NDGAA ++ SE A +G+TP ARIV+ ATAGV+P++MG GP+PA+R+ Sbjct: 239 GTVTAANASGINDGAAGALLMSEAEAVRRGITPLARIVSWATAGVDPQIMGTGPIPASRK 298 Query: 306 VLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMSGAR 365 LE+AG S+ D+D++E NEAFAAQA V +++G D VN NGGAIA+GHP+G SGAR Sbjct: 299 ALEKAGWSVGDLDLVEANEAFAAQACAVNKDMGW--DPSIVNVNGGAIAIGHPIGASGAR 356 Query: 366 LALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399 + E+ RR + L T+CIG G G+AM +E Sbjct: 357 VFNTLVFEMRRRGAKKGLATLCIGGGMGVAMCVE 390 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: 415 Number of extensions: 18 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: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 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 24 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