Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_093393346.1 BM091_RS02955 thiolase family protein
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_900114975.1:WP_093393346.1 Length = 395 Score = 288 bits (736), Expect = 3e-82 Identities = 168/406 (41%), Positives = 238/406 (58%), Gaps = 23/406 (5%) Query: 2 REAFICDGIRTPIGRY--GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59 RE + DGIRT G+ G + RADD+ +RELL RNP++ E +++ + G Q Sbjct: 4 REVVLVDGIRTAFGKAKEDGFFWNTRADDMVVKVIRELLRRNPQVKPEMVEENVWGATTQ 63 Query: 60 AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119 G+ + R +LAGLP SG ++R+C G+ A+ AA I G D+ IAGGVE Sbjct: 64 EGDQGLTIGRTTAILAGLPVECSGFAVDRMCAGGMTAVTCAASEIALGACDIAIAGGVEH 123 Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELL-KISR 178 M P MG A R F+ + + M +TAEN+ ++ +I++ Sbjct: 124 MGHHP--MGATADPNPR------------FLTERIVSEDAL-VMGKTAENLHDMFPEITK 168 Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238 E D +A S ++ AKA G + + IVP+ + K+G V HD+ LRP+ TLE ++ L Sbjct: 169 EMSDEYAYWSHKKAAKAYEEGKIQKTIVPMTVYTKQGWVVA-DHDQQLRPDVTLEGMKNL 227 Query: 239 KAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLG 298 + PFR G +T N+SG+NDGAA +++ S + A G+ P+ R+V A AGV P +MGLG Sbjct: 228 RTPFRVMGKVTPANSSGLNDGAAGVLLMSAEKAKELGIQPKMRLVGYAYAGVHPEVMGLG 287 Query: 299 PVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGL--PDDAPHVNPNGGAIALG 356 P+PAT++VL+R GLS +D+ +IELNEAFA Q L ++E GL PDD +NP GGAIA G Sbjct: 288 PIPATKKVLQRTGLSFNDIGIIELNEAFAVQCLVFMKEFGLKAPDD-ERLNPWGGAIAFG 346 Query: 357 HPLGMSGARLALAASHELHRR-NGRYALCTMCIGVGQGIAMILERV 401 HPL SG RL + H R + RY L TMC+G+GQG A+I E + Sbjct: 347 HPLAASGPRLMIHLMHLFQERPDVRYGLATMCVGLGQGGAVIWENL 392 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: 23 Number of successful extensions: 7 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: 395 Length adjustment: 31 Effective length of query: 370 Effective length of database: 364 Effective search space: 134680 Effective search space used: 134680 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