Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate PP_2137 PP_2137 beta-ketoadipyl CoA thiolase, beta component
Query= BRENDA::Q0K368 (391 letters) >FitnessBrowser__Putida:PP_2137 Length = 391 Score = 254 bits (649), Expect = 3e-72 Identities = 160/397 (40%), Positives = 227/397 (57%), Gaps = 20/397 (5%) Query: 3 EAYIVAAVRTAGGR-KGGKLSGWHPADLAAQVLDALVERTG-ADPALVEDVIMGCVSQVG 60 + IV RT GR KGG D++A ++ L+ER G DP VEDVI GCV+Q Sbjct: 7 DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWGCVNQTL 66 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 EQ N+AR A L + +P + +V R CGSS ALH AAQA+M+G D+ + GVE M Sbjct: 67 EQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMG 126 Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180 V M GV +P + AEM+ + + ++REQ D + L+S Sbjct: 127 HVSMM----------HGVDPNPHLSLHAAKASGMMGLTAEMLGKMHGITREQQDLFGLRS 176 Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVK--LIAEGG 238 HQ A AT G+F EI+P++ +G ++ DE +R + TLE + S+K +GG Sbjct: 177 HQLAHKATVEGKFKDEIIPMQGYDENGFL-KVFDFDETIRPETTLEGLASLKPAFNPKGG 235 Query: 239 RVTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVA 298 VTA ++SQI DGA+ ++V++ LG++PLA + +M V G DP +M P+P+T+ A Sbjct: 236 TVTAGTSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKA 295 Query: 299 LKKAGLRIGDIDLFEVNEAFA----PVPLAWLKATGADPARLNVHGGAIALGHPLGGSGA 354 LK+AGL + DID E+NEAFA PV L LK ++N+HGGAIALGHP G SGA Sbjct: 296 LKRAGLTMADIDFIELNEAFAAQALPV-LKDLKVLDKMDEKVNLHGGAIALGHPFGCSGA 354 Query: 355 KLMTTLVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 ++ TL++ + +G G+ TMC G G T+ ER+ Sbjct: 355 RISGTLLNVMKQNGGTLGVATMCVGLGQGITTVFERV 391 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: 421 Number of extensions: 22 Number of successful extensions: 5 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: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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