Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate 5210417 Shew_2858 acetyl-CoA acetyltransferase (RefSeq)
Query= SwissProt::P09110 (424 letters) >FitnessBrowser__PV4:5210417 Length = 394 Score = 268 bits (686), Expect = 2e-76 Identities = 166/394 (42%), Positives = 231/394 (58%), Gaps = 14/394 (3%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPG- 95 + V+V RT + ++ RG +T +L + ++ + ++ D +G VL G Sbjct: 3 EAVIVSTARTGMAKSFRGSLNNTKSPTMLGHCIKQAVQRAGVEGGEIDDAIMGTVLTAGT 62 Query: 96 AGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSL 155 AG +AR A + +P TV T++RQCSSGL A+ A I I +A G E+++ Sbjct: 63 AGMNIARNAVLAAGLPNTVSAQTIDRQCSSGLMAIGMAAKQIIVDQQQIVVAGGQENITA 122 Query: 156 AD----RGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAA 211 + N +M+ E +PM T+E+VA+ +G+SRE QD +AL SQQ+ A Sbjct: 123 VQNEYMKWAADNADPNVMQFEP--HAYMPMLKTAEHVAKVYGVSREAQDIYALMSQQRTA 180 Query: 212 RAQSKGCFQAEIVPVTTTVH-DDKGTK----RSITVTQDEGIRPSTTMEGLAKLKPAFKK 266 AQ G F EIVP TTT+ D+ TK + +T+ +DE RPSTTME L L P + Sbjct: 181 AAQEAGYFDDEIVPFTTTMAIQDRETKAISYQQVTLDRDECNRPSTTMESLQNLAPVIE- 239 Query: 267 DGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIP 326 G TAGN+SQ+SDGA+A ++ R AE+ GL LG+ R AV G P+ MGIGP YAIP Sbjct: 240 GGFITAGNASQLSDGASACVVMERKLAEQRGLAPLGIYRGIAVAGCAPEEMGIGPIYAIP 299 Query: 327 VALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQ 386 L++ GLT+ D+ ++EINEAFA QA YC + L + P + N GG +++GHP G TG+R Sbjct: 300 KLLKQHGLTIDDIGLWEINEAFAVQALYCRDHLGIDPARYNVNGGGISIGHPYGMTGSRL 359 Query: 387 VITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 V L E KRRG + Y VV MCIG GMGAA +FE Sbjct: 360 VGHALIEGKRRGVK-YVVVGMCIGGGMGAAGLFE 392 Lambda K H 0.317 0.134 0.385 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: 389 Number of extensions: 14 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: 424 Length of database: 394 Length adjustment: 31 Effective length of query: 393 Effective length of database: 363 Effective search space: 142659 Effective search space used: 142659 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 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