Align Acetyl-CoA acetyltransferase; EC 2.3.1.9; Acetoacetyl-CoA thiolase (uncharacterized)
to candidate 6938035 Sama_2168 3-ketoacyl-CoA thiolase (RefSeq)
Query= curated2:P44873 (393 letters) >FitnessBrowser__SB2B:6938035 Length = 436 Score = 223 bits (567), Expect = 1e-62 Identities = 143/424 (33%), Positives = 226/424 (53%), Gaps = 36/424 (8%) Query: 2 ENVVIVSAVRTPIGSFNGALSSVSAVDLGAIVIQEAIKRANIESALVNEVIMGNVLQAGL 61 E + IVS +RTP A VSA+D+G +V+ E + R+ ++ LV +++ G V+Q Sbjct: 13 ERIAIVSGLRTPFAKQATAFHGVSALDMGKMVVNELLSRSELDPKLVEQLVYGQVVQMPA 72 Query: 62 GQNPARQAALKAGIEKEIPSLTINKVCGSGLKSVALGAQSIISGDADIVVVGGMENMSQA 121 N AR+ L G+ + ++ + C + +S A+SI++G+ +I + GG ++ S Sbjct: 73 APNIAREIVLGTGMNVATDAYSVTRACATSFQSTVNIAESIMTGNIEIGIAGGADSSSVL 132 Query: 122 PYLLDSKVRQ-----------GVKMG---NLTLRDTM-IEDGLTCASNHYHMGITAENIA 166 P + K+ G K+ L ++D + + + S MG TAE +A Sbjct: 133 PIGVSKKLAHALVDLTKARTFGQKLAIFRRLGIKDLLPVPPAVAEYSTGLSMGQTAEQMA 192 Query: 167 EQYGISRQAQDELALRSQTLASQAVQLGVFDKEIVPVMVKTRKGDIIVSRDEYPKADTTA 226 + +GISR QD +A RS TLA+Q GV E++ V + + +D + + Sbjct: 193 KTHGISRADQDAMAHRSHTLAAQTWASGVMKNEVMVAHVPPY--NQFIEKDNNIRESSDL 250 Query: 227 EGLAKLKPAF-KKEGTVTAGNASGINDGAAALILVSESKAHALGLKAIAKIRSYASGGVD 285 AKL+P F +K G+VTA N++ + DGA+AL+L+SE +A ALG I I+SYA +D Sbjct: 251 ASYAKLRPVFDRKHGSVTAANSTPLTDGASALLLMSEGRAKALGYTPIGYIKSYAFAAID 310 Query: 286 P-SVMGLGPVPATQKALKKAGINLDDIDLIEANEAFASQFLGVGKDL------------- 331 M +GP AT ALK+AG+ L+D+ LIE +EAFA+Q L K Sbjct: 311 VWEDMLMGPSYATPMALKRAGMQLEDLTLIEMHEAFAAQALANMKMFASKKFAEEKLGQN 370 Query: 332 ----NLDMNKTNIHGGAIALGHPIGASGARILVTLLHNLIEKDKKLGLATLCIGGGQGIS 387 +DM+K N+ GG++A GHP A+GAR++ + + L + +GL T C GG G + Sbjct: 371 RAIGEIDMSKFNVLGGSLAYGHPFAATGARLITQMCNELKRRGGGVGLTTACAAGGLGAA 430 Query: 388 MIVE 391 MI+E Sbjct: 431 MILE 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: 405 Number of extensions: 17 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: 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