Align 3-oxo-acyl CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_011444728.1 SARO_RS05335 acetyl-CoA C-acetyltransferase
Query= metacyc::G185E-7833-MONOMER (386 letters) >NCBI__GCF_000013325.1:WP_011444728.1 Length = 390 Score = 383 bits (984), Expect = e-111 Identities = 212/395 (53%), Positives = 271/395 (68%), Gaps = 14/395 (3%) Query: 1 MTEAYVIDAVRTAVGKRGGALAGIHPVDLGALAWRGLLDRTDIDPAAVDDVIAGCVDAIG 60 M AY++DAVRTA G+RGG LAG+HPVDL A + ++ RT IDP AVDDVI GCV G Sbjct: 1 MATAYIVDAVRTAGGRRGGRLAGVHPVDLAARSLDAIVARTGIDPTAVDDVIMGCVTQAG 60 Query: 61 GQAGNIARLSWLAAGY-PEEVPGVTVDRQCGSSQQAISFGAQAIMSGTADVIVAGGVQNM 119 QA + R + LA+ P+ P VT+DRQCGSSQQAI F AQA+MSG D+++A GV++M Sbjct: 61 QQAMQVGRNAVLASKLLPQSTPAVTIDRQCGSSQQAIQFAAQAVMSGVQDMVIAAGVESM 120 Query: 120 SQIPISSAMTVGEQFG---FTSPTNESKQWLHRYGDQEISQFRGSELIAEKWNLSREEME 176 S++P+ S T + G + SP E K Y SQF G+E+I +K ++++++ Sbjct: 121 SRVPMGSNATFHMKEGLGHYKSPGLEEK-----YPGVMFSQFMGAEMIVKKHGFTKDDLD 175 Query: 177 RYSLTSHERAFAAIRAGHFENEIITVETES--GP--FRVDEGPR-ESSLEKMAGLQPLVE 231 R+SL SH +A AA A F NEI+ VE E+ GP VDEG R +++LE +AG++ L Sbjct: 176 RFSLDSHRKAIAATNAQAFANEIVPVEIETPEGPAMHTVDEGIRFDATLEGIAGVKLLSP 235 Query: 232 GGRLTAAMASQISDGASAVLLASERAVKDHGLRPRARIHHISARAADPVFMLTGPIPATR 291 G LTAA +SQI DG+SAVL+ SE A+K HGL P ARIH+++ A DPV ML P+ AT Sbjct: 236 EGSLTAASSSQICDGSSAVLVVSEAALKAHGLTPLARIHNLTVTAGDPVIMLEEPLFATD 295 Query: 292 YALDKTGLAIDDIDTVEINEAFAPVVMAWLKEIKADPAKVNPNGGAIALGHPLGATGAKL 351 AL + G+ I DID E+NEAFA V MAWLK ADP K+N NGGAIALGHPLGA+G+KL Sbjct: 296 RALQRAGMKISDIDLYEVNEAFASVPMAWLKHTGADPEKLNVNGGAIALGHPLGASGSKL 355 Query: 352 FTTMLGELERIGGRYGLQTMCEGGGTANVTIIERL 386 T++ L GG+YGLQTMCEGGG ANVTIIE L Sbjct: 356 MATLVHALRARGGKYGLQTMCEGGGVANVTIIEAL 390 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: 433 Number of extensions: 19 Number of successful extensions: 4 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: 390 Length adjustment: 30 Effective length of query: 356 Effective length of database: 360 Effective search space: 128160 Effective search space used: 128160 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 Apr 09 2024. 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