Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_011951851.1 SWIT_RS05125 acetyl-CoA C-acyltransferase
Query= metacyc::G185E-7833-MONOMER (386 letters) >NCBI__GCF_000016765.1:WP_011951851.1 Length = 391 Score = 389 bits (998), Expect = e-112 Identities = 207/388 (53%), Positives = 269/388 (69%), Gaps = 7/388 (1%) Query: 4 AYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIGGQA 63 AY++DA+RTA G+R G LAG HP DLG ++ R+ IDP A+DDVI GCV G QA Sbjct: 6 AYIVDALRTAGGRRNGKLAGWHPADLGGAVLDAIVARSGIDPVAIDDVIMGCVSQGGEQA 65 Query: 64 GNIARLSWLAAGYPEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNMSQIP 123 I R + LA+ PE VP V++DRQCGSSQQAI F AQA+MSGT DV++A GV++M+++P Sbjct: 66 FQIGRNAVLASSLPESVPAVSIDRQCGSSQQAIQFAAQAVMSGTQDVVIAAGVESMTRVP 125 Query: 124 ISSAMTVGEQFGFTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEMERYSLTSH 183 + S + EQ G + ++ RY SQF G+E++A K+ LSR++++RY+L SH Sbjct: 126 MFSTGQLFEQAGLGVAKSPGQE--RRYPGIAFSQFVGAEMMARKYGLSRDDLDRYALESH 183 Query: 184 ERAFAAIRAGHFENEIITVE--TESGPF--RVDEGPR-ESSLEKMAGLQPLVEGGRLTAA 238 RA AA+ G F+ EI+ +E T GP DEG R ++SLE + ++ L EGG +TAA Sbjct: 184 RRAAAAVERGDFDAEIVPLEVQTPEGPVFHDRDEGIRFDASLEAIGSVRTLQEGGVVTAA 243 Query: 239 MASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATRYALDKTG 298 ASQI DGASAVL+ SE A+K HGL P ARIH+++ A DPV ML P+ AT AL + G Sbjct: 244 NASQICDGASAVLVVSEAALKAHGLTPLARIHNLTVTAGDPVIMLEEPLIATEKALRRAG 303 Query: 299 LAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKLFTTMLGE 358 + I +ID E+NEAFAPV +AWL+ DP ++N NGGAIALGHPLGA+G KL T++ Sbjct: 304 MTIGEIDLYEVNEAFAPVPLAWLRHSGGDPERLNVNGGAIALGHPLGASGTKLMATLVHA 363 Query: 359 LERIGGRYGLQTMCEGGGTANVTIIERL 386 L R GGRYGLQTMCE GG ANVTI+ERL Sbjct: 364 LRRRGGRYGLQTMCEAGGVANVTIVERL 391 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: 487 Number of extensions: 21 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: 391 Length adjustment: 30 Effective length of query: 356 Effective length of database: 361 Effective search space: 128516 Effective search space used: 128516 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