Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_041096227.1 SUTH_RS00435 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000828635.1:WP_041096227.1 Length = 402 Score = 237 bits (605), Expect = 4e-67 Identities = 158/416 (37%), Positives = 209/416 (50%), Gaps = 36/416 (8%) Query: 1 MTEAVIVSTARTPIGKAYRG-ALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQ 59 MTEA I RTP GK +G ALN L A+ R +D +V+DVV+G Sbjct: 1 MTEAFIFDAVRTPRGKGKQGGALNQATPIYLAATALRALRDRNALDTSKVDDVVLGCVEP 60 Query: 60 QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119 G G +IAR A L A + G T+ R CASGL+A AA ++ ++ VGGG ES Sbjct: 61 VGEQGADIARVAALYADYATSAPGVTVSRFCASGLEACNQAAAQIMSGQADLVVGGGVES 120 Query: 120 ISLVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTA 179 +S V +DP + A V + +A+ +A ++G SR D Y+LESQRR Sbjct: 121 MSRVPMFSSGGAWPIDPQVAAKTAFVPQGI--SADLIATKWGFSRADVDSYALESQRRAK 178 Query: 180 AAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAV--- 236 AA G F I P+ G+ L +DE RPETT E LA LK Sbjct: 179 AAWDAGHFKKSIVPVKDINGLN------------MLDRDEYMRPETTLESLASLKPAFQE 226 Query: 237 RGEGFTIT------------------AGNASQLSDGASATVIMSDKTAAAKGLKPLGIFR 278 +GE + AGN+S + DGA+A + + + AA GLKP R Sbjct: 227 QGENYGFNSVMLQRYPEVERINHVHHAGNSSGIVDGAAAVLFGTKEMGAALGLKPRARIR 286 Query: 279 GMVSYGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEK 338 S G EP M GP +A + LKR G+ V DI L+ELNEAFA VL L + ++ Sbjct: 287 SFASIGSEPSIMLTGPSYAAEKALKRAGMKVGDIDLFELNEAFAAVVLRFMQVLDVSHDR 346 Query: 339 LNVNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 +NVNGGAI++GHP G +GA + G L E RR + T+CVG GMG+A + E V Sbjct: 347 MNVNGGAIAMGHPLGATGAMILGTLLDELERRDLSTGLATLCVGAGMGTATIIERV 402 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: 414 Number of extensions: 11 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: 395 Length of database: 402 Length adjustment: 31 Effective length of query: 364 Effective length of database: 371 Effective search space: 135044 Effective search space used: 135044 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 Apr 09 2024. 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