Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_034998568.1 DL88_RS16315 acetyl-CoA C-acyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_000745425.1:WP_034998568.1 Length = 378 Score = 282 bits (722), Expect = 1e-80 Identities = 169/394 (42%), Positives = 237/394 (60%), Gaps = 18/394 (4%) Query: 1 MKEVVIASAVRTAIGSYGKS-LKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQA 59 M +VVIA +R+ K L V DL A IK V K GI ED+ +++LG Sbjct: 1 MSKVVIAGYLRSPFTLAKKGELATVRPDDLAAQVIKGLVAKTGIPAEDIEDLLLGCAFPE 60 Query: 60 G-LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENM 118 G G N AR SF AGLP+ I A T+N+ CGS + T+ +AA I+ + +A G+E+M Sbjct: 61 GEQGFNIARLVSFIAGLPLSIAAATVNRFCGSSMTTIHMAAGAIQMNAGNAFVAAGVESM 120 Query: 119 SRAPYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEF 178 SR P + N + N + M G + MG TAEN+A +W ISR+EQ+EF Sbjct: 121 SRVPMMGFNP-----LPNPELAASM--PGAYMG-----MGDTAENVAAKWTISRKEQEEF 168 Query: 179 ALASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKD 238 AL S ++A A K G+ DEIV I GRKG ++D P +T+EGLA+LKPAF + Sbjct: 169 ALRSHQRATAAQKEGRLTDEIV--AIAGRKGTIMLDGCIRPE--TTLEGLAELKPAFSAN 224 Query: 239 GTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKA 298 G VTAG +S L D AA +++ S + AK+ + LA I + +G P IMG GP A++ Sbjct: 225 GVVTAGTSSPLTDGAAAVLVCSEDYAKQHKLDVLASIKAIAVSGCSPEIMGIGPVAASRK 284 Query: 299 AIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARIL 358 A+ +AG V ++D++E NEAFA+QS+A ++L +++VN++GGAIALGHP+GA+GARI+ Sbjct: 285 ALARAGLEVSQIDIVELNEAFASQSIACMRELNLSVDRVNIDGGAIALGHPLGATGARIV 344 Query: 359 VTLVHAMQKRDAKKGLATLCIGGGQGTAILLEKC 392 +++ K LAT CIGGGQG A +LE C Sbjct: 345 GKAASLLKREKGKYALATQCIGGGQGIATVLEAC 378 Lambda K H 0.315 0.132 0.375 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: 390 Number of extensions: 15 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: 392 Length of database: 378 Length adjustment: 30 Effective length of query: 362 Effective length of database: 348 Effective search space: 125976 Effective search space used: 125976 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 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