Align Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate WP_013135151.1 ARNIT_RS06730 acetyl-CoA C-acyltransferase
Query= curated2:P44873 (393 letters) >NCBI__GCF_000092245.1:WP_013135151.1 Length = 423 Score = 286 bits (732), Expect = 8e-82 Identities = 171/424 (40%), Positives = 253/424 (59%), Gaps = 38/424 (8%) Query: 2 ENVVIVSAVRTPIGSFNGALSSVSAVDLGAIVIQEAIKRANIESALVNEVIMGNVLQAGL 61 E + I+ +R+P+ NG L++VSA LGAI+ +E + R NI +EVI+GNV Q Sbjct: 3 ERIAIIDGLRSPVAKANGKLNNVSADSLGAIIAKELVLRNNIPYDDFDEVIIGNVAQPAN 62 Query: 62 GQNPARQAALKAGIEKEIPSLTINKVCGSGLKSVALGAQSIISGDADIVVVGGMENMSQA 121 N AR A++AG K+ + T+++ C SG+++++ + I + I + GG+E+MS Sbjct: 63 AANIARVLAMRAGFPKKTIAYTVHRNCASGMQALSSSIEKIYTKQGKIYLAGGVESMSNI 122 Query: 122 PYLLDSKVRQGV-----------KMGNLT------LRDTM-IEDGLTCASNHYHMGITAE 163 P L ++ + + K+ LT L+ T+ + GLT + MGITAE Sbjct: 123 PLLFSNQFKDFMTKFTYAKSTSEKLKLLTSFRLSFLKPTIGLISGLTDPISGKIMGITAE 182 Query: 164 NIAEQYGISRQAQDELALRSQTLASQAVQLGVFDKEIVPVMVKTRKGDIIVSRDEYPKAD 223 N+A ++ ISRQAQDE +L+S A +A++ G+ + EI P+M K D + D+ + + Sbjct: 183 NLANEFKISRQAQDEYSLQSHLKAQKAIESGILNDEIHPIMTK----DSSIMDDDGIRFN 238 Query: 224 TTAEGLAKLKPAFKKEGTVTAGNASGINDGAAALILVSESKAHALGLKAIAKIRSYASGG 283 T + L KLKP F + GTVTAGN+S ++DGA +IL SESKA LGL+ I I+ YA G Sbjct: 239 QTIQALNKLKPIFDRNGTVTAGNSSQVSDGACMMILCSESKAKELGLEPIGFIKDYAYAG 298 Query: 284 VDPSVMGLGPVPATQKALKKAGINLDDIDLIEANEAFASQFLG----------VGKDLN- 332 +D + MGLGP+ AT+K K G++L +IDLIE NEAFA+Q + K+ N Sbjct: 299 LDANKMGLGPIFATKKLFDKTGVSLKNIDLIELNEAFAAQVIANLEAFKSKSFCKKEFNS 358 Query: 333 -----LDMNKTNIHGGAIALGHPIGASGARILVTLLHNLIEKDKKLGLATLCIGGGQGIS 387 ++ N++GGAIA+GHP+G SGARI++ + L K K GLATLC+GGGQG S Sbjct: 359 EPLGEINEEILNVNGGAIAIGHPVGMSGARIVLHTVKELKRKGLKTGLATLCVGGGQGAS 418 Query: 388 MIVE 391 +VE Sbjct: 419 FLVE 422 Lambda K H 0.315 0.133 0.360 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: 431 Number of extensions: 25 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: 393 Length of database: 423 Length adjustment: 31 Effective length of query: 362 Effective length of database: 392 Effective search space: 141904 Effective search space used: 141904 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: 42 (22.0 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