Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_011952838.1 SWIT_RS10105 acetyl-CoA C-acyltransferase
Query= metacyc::G185E-7833-MONOMER (386 letters) >NCBI__GCF_000016765.1:WP_011952838.1 Length = 393 Score = 362 bits (930), Expect = e-105 Identities = 197/395 (49%), Positives = 254/395 (64%), Gaps = 22/395 (5%) Query: 6 VIDAVRTAVG--KRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIGGQA 63 ++D VRT +G K+GG L+ +HPVDL A A + L++R D+DPA VDDVI GCV +G Q+ Sbjct: 7 IVDIVRTPLGRGKQGGQLSQVHPVDLLATALKALVERNDLDPAMVDDVITGCVSQVGEQS 66 Query: 64 GNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMSQIP 123 R++WL AG+P VP T+DR+CGSSQQAI F AQ I +G D+++A GV++MS++P Sbjct: 67 ATPGRVAWLGAGFPAHVPSTTIDRKCGSSQQAIHFAAQGIAAGAYDIVIAAGVESMSRVP 126 Query: 124 ISSAMTVGEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERYSLTSH 183 + S + +G R+ + Q +ELIA +W + REEM+ YS+ SH Sbjct: 127 MGSNRIGQDPYG--------PAMAERFPQGLVQQGISAELIAARWGIGREEMDAYSVESH 178 Query: 184 ERAFAAIRAGHFENEIITVETESGPFRVDEGPRE-SSLEKMAGLQPLVEGGR-------- 234 RA A AG F++EII V + DE R +S + +A L+P E Sbjct: 179 SRAAAVRDAGGFDDEIIPVFADGASIVSDETIRPGTSPDALAQLKPAFERPEFAQRFPEI 238 Query: 235 ---LTAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATR 291 +TA ASQISDGA+A LL SER GLRPRAR R DP+ MLT PIPATR Sbjct: 239 RWSVTAGNASQISDGAAAALLMSERTATRLGLRPRARFVAFDVRGDDPLLMLTAPIPATR 298 Query: 292 YALDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKL 351 L+K L ++ ID E+NEAFA V +AWLKE+KADPA++NP GGAIALGHPLGA+G +L Sbjct: 299 RVLEKADLRVEAIDHFEVNEAFACVPLAWLKELKADPARLNPRGGAIALGHPLGASGIRL 358 Query: 352 FTTMLGELERIGGRYGLQTMCEGGGTANVTIIERL 386 TMLG LE+ GGR+GLQTMCE GG AN TIIERL Sbjct: 359 MATMLGALEQGGGRFGLQTMCEAGGMANATIIERL 393 Lambda K H 0.317 0.134 0.389 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: 445 Number of extensions: 16 Number of successful extensions: 3 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: 386 Length of database: 393 Length adjustment: 30 Effective length of query: 356 Effective length of database: 363 Effective search space: 129228 Effective search space used: 129228 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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