Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate Pf1N1B4_3904 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= BRENDA::Q0K368 (391 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3904 Length = 383 Score = 261 bits (666), Expect = 3e-74 Identities = 162/394 (41%), Positives = 233/394 (59%), Gaps = 20/394 (5%) Query: 6 IVAAVRTAGGR-KGGKLSGWHPADLAAQVLDALVERT-GADPALVEDVIMGCVSQVGEQA 63 IV RT GR KGG D++A ++ L+ER DP+ VEDVI GCV+Q EQ Sbjct: 2 IVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTLEQG 61 Query: 64 GNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMTRVP 123 N+AR A L +++P + G +V R CGSS ALH AAQA+M+G D+ + GVE M V Sbjct: 62 WNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVS 121 Query: 124 MGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQSHQR 183 M GV +P + AEM+ + + ++REQ DA+ ++SHQ Sbjct: 122 MM----------HGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREQQDAFGVRSHQL 171 Query: 184 AIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVK--LIAEGGRVT 241 A AT G+F EI+P++ +G ++ DE +R + TLES+ ++K +GG VT Sbjct: 172 AHKATLEGKFKDEIIPMQGYDENGFL-KLFDYDETIRPETTLESLAALKPAFNPKGGTVT 230 Query: 242 AASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVALKK 301 A ++SQI DGA+ ++V++ + LG++P+A + +M V G DP +M P+PAT+ ALK+ Sbjct: 231 AGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVPATQKALKR 290 Query: 302 AGLRIGDIDLFEVNEAFA----PVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLM 357 AGL I DID FE+NEAFA PV L LK ++N+HGGAIALGHP G SGA++ Sbjct: 291 AGLGINDIDFFELNEAFAAQALPV-LKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARIS 349 Query: 358 TTLVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 TL++ + +G +G+ TMC G G T+ ER+ Sbjct: 350 GTLLNVMKQNGGTFGVATMCIGLGQGISTVFERV 383 Lambda K H 0.317 0.132 0.379 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: 412 Number of extensions: 21 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: 391 Length of database: 383 Length adjustment: 30 Effective length of query: 361 Effective length of database: 353 Effective search space: 127433 Effective search space used: 127433 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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