Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_012645203.1 GEOB_RS00490 acetyl-CoA C-acyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_000022265.1:WP_012645203.1 Length = 399 Score = 360 bits (924), Expect = e-104 Identities = 192/399 (48%), Positives = 265/399 (66%), Gaps = 8/399 (2%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60 M + VIV A RT VGK+GG+L + + +L A I ++R + P + +V++G AG Sbjct: 1 MREAVIVDAVRTPVGKWGGALKNVRSDDLAAHCIAELVKRTKIDPNLIEDVVLGCTNQAG 60 Query: 61 S-GQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMS 119 +N R AA+ AGLP TIN++C SGL A+ AA AI G+ ++ +AGG E+M+ Sbjct: 61 EDNRNVGRMAALLAGLPYSAAGQTINRLCASGLNAINSAAQAIKVGEGDVFIAGGTESMT 120 Query: 120 AAPHVLPGSRDGFRMGDAKLVDTMIV-----DGLWDVYNQYHMGITAENVAKEYGITREA 174 AP V+ S F D K+ DT+I + + Y + MG TAENVA YG+TR+ Sbjct: 121 RAPFVMAKSESPFSR-DVKVFDTVIGWRFTNPKMTEPYAKEGMGETAENVAVRYGLTRQE 179 Query: 175 QDEFAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVR-QGATLDSMSGLK 233 QDEFA+ +Q K AA AGKF++EIVPV+IPQ+KGDP+ DEF R T++ ++ L Sbjct: 180 QDEFALDTQKKWAAADAAGKFNDEIVPVVIPQKKGDPIIVSRDEFPRGNDVTMEQLAKLP 239 Query: 234 PAFDKAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGP 293 AF K GTVTA N+SG+NDGAAA+++M A AK+LG PLA + + A AG DP MG+GP Sbjct: 240 AAFRKDGTVTAGNSSGINDGAAALLLMEAETAKKLGYKPLARVVASAVAGCDPSYMGLGP 299 Query: 294 VPASKRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGA 353 +PA ++ L RA +D+DL E+NEAFAAQ++ +++G D +KVNVNGG+IAIGHP+G+ Sbjct: 300 IPAIQKVLKRANLKIEDIDLFELNEAFAAQSIPCIRELGIDPAKVNVNGGSIAIGHPLGS 359 Query: 354 SGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392 +G RI TL+HEMKRR+A+ G+ SLCIG G G+A ER Sbjct: 360 TGARITATLVHEMKRRNARYGIVSLCIGVGQGIATVFER 398 Lambda K H 0.315 0.131 0.369 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: 392 Number of extensions: 12 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: 393 Length of database: 399 Length adjustment: 31 Effective length of query: 362 Effective length of database: 368 Effective search space: 133216 Effective search space used: 133216 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