Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_012784175.1 AFER_RS00420 acetyl-CoA C-acyltransferase
Query= BRENDA::Q0K368 (391 letters) >NCBI__GCF_000023265.1:WP_012784175.1 Length = 391 Score = 419 bits (1078), Expect = e-122 Identities = 228/395 (57%), Positives = 284/395 (71%), Gaps = 9/395 (2%) Query: 1 MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60 M +A IV VRT GR+ G LSGWH DLA+ VL+ALV RTG DPALVEDVIMGCVSQVG Sbjct: 1 MRDAVIVDVVRTPVGRRNGALSGWHAVDLASTVLEALVARTGIDPALVEDVIMGCVSQVG 60 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 EQ NVARNA+LA+ PESVPGT+VDRQCGSSQQA+ FAAQ V++GA D+VIAAGVESM+ Sbjct: 61 EQGINVARNAVLAAGFPESVPGTTVDRQCGSSQQAVAFAAQGVLAGAYDVVIAAGVESMS 120 Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYP--GVQFSQFTGAEMIARKYDLSREQLDAYAL 178 RVPMG + P G P P +EARY G Q AE+I ++ L+R++LDA+AL Sbjct: 121 RVPMGSNGVGP-----GSPFGPRVEARYAARGGLVPQGISAELIVERWGLTRQELDAFAL 175 Query: 179 QSHQRAIAATKSGRFTAEILPVEVRTADGANG-EMHTTDEGVRYDATLESIGSVK-LIAE 236 +SH+RA AT GRF +EILP+E R ADGA + DEG+R D +LE++GS+K Sbjct: 176 RSHERAWTATTEGRFKSEILPIEGRRADGAAAPTVLEADEGIRPDTSLEALGSLKPAFVP 235 Query: 237 GGRVTAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATE 296 G VTA +ASQI DGAA ++++ ++LG+ P ARV A ++ DP++ML AP+PAT Sbjct: 236 TGTVTAGNASQISDGAAAALIMDAERARRLGLVPRARVVAFSLAADDPIMMLTAPIPATR 295 Query: 297 VALKKAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKL 356 L++A L + DIDL E+NEAFA V LAW D R+NV+GGAIALGHPLG SGA+L Sbjct: 296 RVLERAHLSLDDIDLVEINEAFASVVLAWGAELHPDWDRVNVNGGAIALGHPLGASGARL 355 Query: 357 MTTLVHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 + TLV+ L G RYGLQTMCEGGG+AN ++ERL Sbjct: 356 LATLVNELERRGGRYGLQTMCEGGGMANALVIERL 390 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: 479 Number of extensions: 24 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: 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 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