Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_011779834.1 MVAN_RS13145 acetyl-CoA C-acyltransferase
Query= BRENDA::Q0KAI3 (392 letters) >NCBI__GCF_000015305.1:WP_011779834.1 Length = 394 Score = 420 bits (1080), Expect = e-122 Identities = 220/395 (55%), Positives = 282/395 (71%), Gaps = 11/395 (2%) Query: 2 QQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQA 61 + AVIV A+R+P+G+ K A ++ +LLA ++ +V R +DP VDDVI G VTQ Sbjct: 7 RDAVIVAAVRTPVGKGKANGALHDVLPADLLAHSLREVVTRAGVDPAEVDDVIAGAVTQV 66 Query: 62 GEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIESM 121 G+Q+ R A L AGFP+ VP TT+DR+CGSSQQA+ FAAQG++AGAYDIVIA G+ESM Sbjct: 67 GDQAVNIARNALLGAGFPESVPGTTVDRQCGSSQQAISFAAQGVLAGAYDIVIAAGVESM 126 Query: 122 SRVPMGSARI-GQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHELA 180 SRVPMGS+ + G NP+G M RY GLV+QGV+AEL+AAK+ LSR +D +SA SH+ A Sbjct: 127 SRVPMGSSVLPGSNPFGTGMAERYPEGLVAQGVSAELIAAKWNLSRTQLDEFSAESHQKA 186 Query: 181 ATARESGAFRRE---ILGISTPNGLVEQDETIRPGTSVEKLGTLQASFRNDELSARFPQI 237 A A + G F E I G+ST DE IRP T+VE L L+ +F N+ + ARFPQI Sbjct: 187 ARATKDGLFDHELAPIAGLST-------DEIIRPDTTVETLAGLRPAFYNEAIGARFPQI 239 Query: 238 GWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIPASQ 297 GWN+T GN+S +SDG++A+L+ S + A+RLGL+P AR G DP+ MLT IPA++ Sbjct: 240 GWNITPGNSSPLSDGSAAVLITSGAAARRLGLRPLARIHTTVAVGSDPLYMLTGVIPATE 299 Query: 298 RAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHPLGASGVRL 357 + + +SGL L ID +E+NEAFA V LAW R GAD AR N GGAIA+GHPLGASG R+ Sbjct: 300 KVLARSGLSLSDIDLFEVNEAFAPVVLAWARDTGADLARTNVHGGAIAIGHPLGASGARI 359 Query: 358 MTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392 MTT+++ALE RY LQ+MCE GGMANATIIERL Sbjct: 360 MTTLVNALEQRDGRYALQTMCEGGGMANATIIERL 394 Lambda K H 0.318 0.132 0.384 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: 501 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: 392 Length of database: 394 Length adjustment: 31 Effective length of query: 361 Effective length of database: 363 Effective search space: 131043 Effective search space used: 131043 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 (21.7 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