Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ga0059261_2160 Ga0059261_2160 acetyl-CoA acetyltransferases
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Korea:Ga0059261_2160 Length = 398 Score = 428 bits (1100), Expect = e-124 Identities = 225/399 (56%), Positives = 276/399 (69%), Gaps = 8/399 (2%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M EA IVSTART IGKAYRGA N TE L GH + AV+RAG+DP ++D+ G Q Sbjct: 1 MREAAIVSTARTGIGKAYRGAFNTTEAPVLAGHVMNAAVERAGVDPARIDDIFWGVGNQW 60 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G GGN R A+ AGLP + T+DR+C SGL A+ALAARS++ ++IA+ GG ESI Sbjct: 61 GTQGGNAGRMAVFAAGLPQSVPAFTLDRKCGSGLTALALAARSIIAGDIDIALSGGMESI 120 Query: 121 SLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAA 180 SL + + ++ A + YM M++TAE VA+RYGISR RQDEY SQ+R A Sbjct: 121 SLTVTKDAPRY--ANQSVLANEPHAYMPMIETAEIVAERYGISRARQDEYGAMSQQRAEA 178 Query: 181 AQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRG-- 238 G F +EIAPI+ + + DK + +T++QDEG R TTAE LAGLK V Sbjct: 179 GLASGAFAEEIAPITVEKAIFDKEGNRTGSERVTVTQDEGIRAGTTAEALAGLKTVWKDG 238 Query: 239 ----EGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGP 294 EG ITAGNASQLSDGA+A ++M A A+G + LGI+RG + GC PDEMGIGP Sbjct: 239 QVVKEGRHITAGNASQLSDGAAAQIVMDRAIAEAEGKEILGIYRGFQAAGCAPDEMGIGP 298 Query: 295 VFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGM 354 VFA+P+LL R GL V DIGLWELNEAFA Q LYCRD LGIDPEK NVNGGAI++GHP+GM Sbjct: 299 VFAIPKLLGRAGLEVADIGLWELNEAFASQCLYCRDTLGIDPEKYNVNGGAIAIGHPFGM 358 Query: 355 SGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEI 393 +GARL GHALIEGR+R ++ VV+MC GGMG+AGLFEI Sbjct: 359 TGARLIGHALIEGRKRGVRWVVVSMCTAGGMGAAGLFEI 397 Lambda K H 0.316 0.134 0.378 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: 515 Number of extensions: 21 Number of successful extensions: 3 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: 395 Length of database: 398 Length adjustment: 31 Effective length of query: 364 Effective length of database: 367 Effective search space: 133588 Effective search space used: 133588 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 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