Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_089217008.1 CHB69_RS16345 acetyl-CoA C-acyltransferase
Query= BRENDA::Q0K368 (391 letters) >NCBI__GCF_900188185.1:WP_089217008.1 Length = 389 Score = 497 bits (1280), Expect = e-145 Identities = 248/391 (63%), Positives = 305/391 (78%), Gaps = 2/391 (0%) Query: 1 MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60 MA AYIV AVRTAGGR+GG+L+G HP DL A V DA+ +R D A ++DVI GCVSQ G Sbjct: 1 MAAAYIVDAVRTAGGRRGGRLAGVHPVDLGAAVYDAIADRNDFDTAAIDDVITGCVSQGG 60 Query: 61 EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120 EQ ++ RNA+LAS+LP+S+P ++DRQCGSSQQA+ FAAQAVMSG DIV+A+G+ESMT Sbjct: 61 EQTMDLGRNAVLASKLPDSIPAVTIDRQCGSSQQAMMFAAQAVMSGTQDIVLASGIESMT 120 Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180 RVPMG + L K G G KSP +E +YPG+ FSQF GAEMI +K+ +++ LDA+AL+S Sbjct: 121 RVPMGSVATLFMKEGLGNYKSPRLEEKYPGIMFSQFMGAEMIVKKHGFTKDDLDAFALES 180 Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLIAEGGRV 240 H+RA AAT+ G+F EI+P+ + T +GA MH DEG+R+DATLE I VKL+ EGG + Sbjct: 181 HRRARAATEGGKFEREIVPIAIETPEGA--AMHKVDEGIRFDATLEGIAGVKLLQEGGTI 238 Query: 241 TAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVALK 300 TAAS+SQICDGA+ ++V+E LK G+ P AR+H ++V DPV+MLE PL ATE ALK Sbjct: 239 TAASSSQICDGASAALIVSEQALKDHGLTPRARIHHISVTAGDPVIMLEEPLFATEKALK 298 Query: 301 KAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTTL 360 KAG++IGDID +EVNEAFAPVPLAW+K GAD ARLNVHGGAIALGHPLG SG KLM TL Sbjct: 299 KAGMKIGDIDAYEVNEAFAPVPLAWMKYLGADHARLNVHGGAIALGHPLGASGTKLMATL 358 Query: 361 VHALHTHGKRYGLQTMCEGGGLANVTIVERL 391 + L G +YGLQTMCEGGG ANVTIVERL Sbjct: 359 LGVLDATGGKYGLQTMCEGGGQANVTIVERL 389 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: 531 Number of extensions: 21 Number of successful extensions: 2 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: 389 Length adjustment: 31 Effective length of query: 360 Effective length of database: 358 Effective search space: 128880 Effective search space used: 128880 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