Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate GFF4003 HP15_3943 acetyl-CoA C-acyltransferase
Query= SwissProt::P09110 (424 letters) >FitnessBrowser__Marino:GFF4003 Length = 365 Score = 256 bits (655), Expect = 6e-73 Identities = 152/361 (42%), Positives = 224/361 (62%), Gaps = 10/361 (2%) Query: 68 VMTAVLKDVNLRPEQLGDICVGNVLQPGA-GAIMARIAQFLSDIPETVPLSTVNRQCSSG 126 V+ ++ + P + D+ +G Q GA G +AR+A + +P T ++NR CSSG Sbjct: 5 VIKHAVERAGIDPSIVEDVIMGAAYQEGAQGRNIARLAAIRAGLPVTTAGFSINRFCSSG 64 Query: 127 LQAVASIAGGIRNGSYDIGMACGVESMSLA--DRGNPGNITSRLMEKEKARDCLIPMGIT 184 LQ++A A + + +A GVES+SL ++ N + T+ + K K + + M T Sbjct: 65 LQSIALAAQRVVSEKVPAMVAGGVESISLVQNEKINSFHATNEWLMKNKP-ELYLSMIET 123 Query: 185 SENVAERFGISREKQDTFALASQQKAARAQSKGCFQAEIVPVTTTVH-DDKGT----KRS 239 ++ VA+R+ +SRE QD ++L SQQ+ A AQ G F EIVP T+ DK T ++ Sbjct: 124 ADIVAKRYNVSREAQDEYSLISQQRTAAAQQAGKFDDEIVPFDATMLVKDKETGEVSEKQ 183 Query: 240 ITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLP 299 +T+ DE RP+TT+EGLA L+P + TAGN+SQ+SDGA+ + + AE+ + Sbjct: 184 VTLKGDECNRPNTTLEGLAGLEPVRGPEQFITAGNASQLSDGASVCTVMNSTYAEKHNIE 243 Query: 300 ILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKL 359 +G+ R +AV G PD MGIGP YAIP L++ GLT+ D+D++E+NEAFASQ YC ++L Sbjct: 244 PMGIFRGFAVAGCEPDEMGIGPVYAIPRLLERNGLTMDDIDLWELNEAFASQVIYCRDRL 303 Query: 360 RLPPEKVNPLGGAVALGHPLGCTGARQVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVF 419 +P EK+N GG++++GHP G TGARQ L E KRRG + Y V++MCIG G GAA +F Sbjct: 304 GIPMEKLNVNGGSISIGHPFGVTGARQTGHALIEGKRRGAK-YVVITMCIGGGQGAAGLF 362 Query: 420 E 420 E Sbjct: 363 E 363 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: 378 Number of extensions: 16 Number of successful extensions: 4 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: 365 Length adjustment: 31 Effective length of query: 393 Effective length of database: 334 Effective search space: 131262 Effective search space used: 131262 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