Align propanoyl-CoA C-acyltransferase (EC 2.3.1.176) (characterized)
to candidate WP_013644968.1 METBO_RS06870 acetyl-CoA acetyltransferase
Query= BRENDA::P22307 (547 letters) >NCBI__GCF_000191585.1:WP_013644968.1 Length = 383 Score = 233 bits (593), Expect = 1e-65 Identities = 147/395 (37%), Positives = 198/395 (50%), Gaps = 22/395 (5%) Query: 11 LRRVFVVGVGMTKFVKPGAENSRDYPDLAEEAGKKALADAQIPYSAVDQACVGYVFGDST 70 +R V ++GV TKF G + D+ EAG KA+ DA I ++ VG + Sbjct: 1 MRDVAIIGVSQTKF---GELWEVSFRDMITEAGMKAIGDAGIEGDELEAMYVGNMSAGLF 57 Query: 71 CGQRAIYHSL----GMTGIPIINVNNNCATGSTALFMARQLIQGGVAECVLALGFEKMSK 126 Q I + G+T IP V CA+G AL + G + V++ G EKM+ Sbjct: 58 VEQEHIASLIADHAGLTPIPSARVEAACASGGLALRNGIMAVASGYHDIVISAGVEKMT- 116 Query: 127 GSLGIKFSDRTIPTDKHVDLLINKYGLSAHPVAPQMFGYAGKEHMEKYGTKIEHFAKIGW 186 D PT ++ P ++ K HM +YGT E A + Sbjct: 117 --------DVVDPTPAIATASDQEWEAQQGVTFPSLYAMMAKRHMHEYGTTREQLAMVSV 168 Query: 187 KNHKHSVNNPYSQFQDEYSLDEVMASKEVFDFLTILQCCPTSDGAAAAILASEAFVQKYG 246 NHKH NP +Q+ E S+D V+ S V D L +L C P SDGAAA IL +KY Sbjct: 169 LNHKHGAKNPLAQYPMEISVDSVLNSSIVADPLRLLDCSPVSDGAAAVILCPAEDARKY- 227 Query: 247 LQSKAVEILAQEMMTDLPSSFEEKSIIKMVGFDMSKEAARKCYEKSGLTPNDIDVIELHD 306 V + A + + + K I + D + A+RK YE SG TP DI +E+HD Sbjct: 228 -TDTPVYVKASTQASGTIALHDRKDITTI---DSTVNASRKAYEISGYTPKDIGGVEVHD 283 Query: 307 CFSTNELLTYEALGLCPEGQGATLVDRGDNTYGGKWVINPSGGLISKGHPLGATGLAQCA 366 CFS N LL E LG +GQG ++ G G+ +NPSGGL ++GHPLGATG+AQ A Sbjct: 284 CFSINGLLAIEDLGFVEKGQGGPAIEDGMTELDGEIPVNPSGGLKARGHPLGATGIAQAA 343 Query: 367 ELCWQLRGEAGKRQVPGAKVALQHNL-GIGGAVVV 400 E+ WQLRGEAGKRQ+ G +V + HN+ G GG V Sbjct: 344 EIVWQLRGEAGKRQIEGIEVGMTHNIGGTGGTAAV 378 Lambda K H 0.317 0.134 0.395 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: 518 Number of extensions: 22 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: 547 Length of database: 383 Length adjustment: 33 Effective length of query: 514 Effective length of database: 350 Effective search space: 179900 Effective search space used: 179900 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: 51 (24.3 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