Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate PP_2051 PP_2051 3-ketoacyl-CoA thiolase (thiolase I)
Query= SwissProt::P09110 (424 letters) >FitnessBrowser__Putida:PP_2051 Length = 394 Score = 278 bits (712), Expect = 2e-79 Identities = 166/393 (42%), Positives = 233/393 (59%), Gaps = 12/393 (3%) Query: 37 DVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGA 96 D V+V RT I +A RG F D + + + A ++ + P Q+ D+ +G +Q G Sbjct: 3 DAVIVATARTPIGKAMRGAFNDLKTPSMTAVAIRAAVERAGIEPAQVDDLVLGTAMQSGT 62 Query: 97 GAIM-ARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSL 155 AI R++ + +P++V TV+RQC+SGL A+A+ A I + + G E +SL Sbjct: 63 AAINPGRLSALAAGLPQSVSGQTVDRQCASGLMAIATAAKQIMVDGMQVTIGAGQEQISL 122 Query: 156 ADRGNPGNITSRLMEKEKAR---DCLIPMGITSENVAERFGISREKQDTFALASQQKAAR 212 + + + S + R +PM T+E VA R+GISRE QD +AL SQQ+ A Sbjct: 123 VQQVH-NQLASEAYDPAVLRMSEHAYMPMLQTAERVARRYGISREAQDVYALQSQQRTAA 181 Query: 213 AQSKGCFQAEIVPVTTTVHD-DKGT----KRSITVTQDEGIRPSTTMEGLAKLKPAFKKD 267 AQ+ G F AEIVPV DK T + +TQDEG RP+TT+ L LKP + Sbjct: 182 AQAAGLFAAEIVPVIARKKVVDKLTGVVSHEEVRLTQDEGNRPATTLADLQGLKPVVE-G 240 Query: 268 GSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPV 327 G TAGN+SQ+SDGA+A +L + A G+ LG+ R AV G+ P+ MGIGP A+P Sbjct: 241 GCVTAGNASQLSDGASACVLMEGALAARSGIAALGLYRGIAVAGLAPEEMGIGPVLAVPK 300 Query: 328 ALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQV 387 L++ GLTV D+ ++E+NEAFA Q YC ++L++ P K+N GGA+A+GHP G +GAR V Sbjct: 301 LLRQQGLTVDDIGLWELNEAFACQVLYCAQQLQIDPAKLNVNGGAIAIGHPYGMSGARMV 360 Query: 388 ITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFE 420 L E KRR K Y VV+MC+G GMGAA +FE Sbjct: 361 GHALLEGKRR-KVKYVVVTMCVGGGMGAAGLFE 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: 426 Number of extensions: 22 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