Align Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate 5209978 Shew_2426 3-ketoacyl-CoA thiolase (RefSeq)
Query= curated2:P44873 (393 letters) >FitnessBrowser__PV4:5209978 Length = 436 Score = 223 bits (569), Expect = 6e-63 Identities = 142/424 (33%), Positives = 227/424 (53%), Gaps = 36/424 (8%) Query: 2 ENVVIVSAVRTPIGSFNGALSSVSAVDLGAIVIQEAIKRANIESALVNEVIMGNVLQAGL 61 + + IV +RTP A VSA+D+G +V+ E + R+ ++ + +++ G V+Q Sbjct: 13 DRIAIVMGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKEIEQLVYGQVVQMPA 72 Query: 62 GQNPARQAALKAGIEKEIPSLTINKVCGSGLKSVALGAQSIISGDADIVVVGGMENMSQA 121 N AR+ L G+ + ++ + C + +S A+SI++G+ +I + GG ++ S Sbjct: 73 APNIAREIVLGTGMNVSTDAYSVTRACATSFQSTVNVAESIMTGNIEIGIAGGADSSSVL 132 Query: 122 PYLLDSKVRQGVK--------------MGNLTLRDTM-IEDGLTCASNHYHMGITAENIA 166 P + K+ + + L L+D + + + S MG TAE +A Sbjct: 133 PIGVSKKLAHALVDLNKARSFGQKWAIIRRLGLKDLLPVPPAVAEYSTGLSMGQTAEQMA 192 Query: 167 EQYGISRQAQDELALRSQTLASQAVQLGVFDKEIVPVMVKTRKGDIIVSRDEYPKADTTA 226 + Y ISR QD LA RS TLA++ G E++ V K + RD + +++ Sbjct: 193 KTYNISRADQDALAHRSHTLATETWDSGHLRDEVMVAHVPPYKS--FIDRDNNIRENSSL 250 Query: 227 EGLAKLKPAF-KKEGTVTAGNASGINDGAAALILVSESKAHALGLKAIAKIRSYASGGVD 285 + AKL+PAF +K G+VTA N++ + DGA+A++L+SES+A ALG + I I+SYA +D Sbjct: 251 DSYAKLRPAFDRKHGSVTAANSTPLTDGASAVLLMSESRAKALGYEPIGYIKSYAFSAID 310 Query: 286 P-SVMGLGPVPATQKALKKAGINLDDIDLIEANEAFASQFLG--------------VGKD 330 M +GP AT ALK+AG+ L+D+ LIE +EAFA+Q L +G+D Sbjct: 311 VWQDMLMGPSYATPLALKRAGMELEDLTLIEMHEAFAAQTLANMQMFASKKFAKEKLGRD 370 Query: 331 L---NLDMNKTNIHGGAIALGHPIGASGARILVTLLHNLIEKDKKLGLATLCIGGGQGIS 387 +DM K N+ GG++A GHP A+G R++ + L + GLAT C GG G + Sbjct: 371 RAIGEIDMTKFNVLGGSLAYGHPFAATGTRLITQVCRELKRRGGGTGLATACAAGGLGAA 430 Query: 388 MIVE 391 MIVE Sbjct: 431 MIVE 434 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: 416 Number of extensions: 16 Number of successful extensions: 6 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: 436 Length adjustment: 31 Effective length of query: 362 Effective length of database: 405 Effective search space: 146610 Effective search space used: 146610 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 17 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