Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__Cola:Echvi_1071 Length = 391 Score = 281 bits (720), Expect = 2e-80 Identities = 167/406 (41%), Positives = 238/406 (58%), Gaps = 28/406 (6%) Query: 3 EAFICDGIRTPIGRYG-GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAG 61 +A+I G RT +G+ G R DDLA +++L+ P L+AE +DD+I+G A Sbjct: 2 DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61 Query: 62 EDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMS 121 E + RM +L+A L + V G INR CGSGL+A+ A IK+G D +IAGG ESMS Sbjct: 62 EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120 Query: 122 RAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQ 181 P +MG + T + W+ + SM TAE +A+ ISRED Sbjct: 121 MVP-MMG------------YKTALNWKIASEHPDYYL---SMGLTAEELAKDYDISREDS 164 Query: 182 DSFALRSQQRTAKAQSSGILAEEIVPVVLKN--------KKGVVTEIQHDEHLRPETTLE 233 D FA+ S +R A G EEIVP+ ++ ++ + DE RP T ++ Sbjct: 165 DQFAVTSHERAISAIKEGRFKEEIVPIEVEETFVDASGKRQTRTFTVDTDEGPRPGTNMD 224 Query: 234 QLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPR 293 L GLK F+ G +TAGN+S +DGAA ++ SE+M L P AR+V+ + AGV+PR Sbjct: 225 VLGGLKPAFKQGGQVTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPR 284 Query: 294 LMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAI 353 +MG+GP A + L++AG+ + D+ ++ELNEAFAAQAL V+R L + D VN NGGA+ Sbjct: 285 IMGIGPKEAVPKALKQAGMKMSDISLVELNEAFAAQALAVIRALDM--DPNTVNVNGGAV 342 Query: 354 ALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILE 399 ALGHPLG +GA+L + +EL RRN +Y + T C+G GQG+A ++E Sbjct: 343 ALGHPLGCTGAKLTVQMINELRRRNQKYGMVTACVGGGQGVAGVVE 388 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: 411 Number of extensions: 18 Number of successful extensions: 5 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: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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