Align 3-ketoacyl-CoA thiolase B, peroxisomal; Acetyl-CoA acyltransferase B; Beta-ketothiolase B; Peroxisomal 3-oxoacyl-CoA thiolase B; EC 2.3.1.155; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_051463071.1 HALAL_RS0110640 acetyl-CoA C-acyltransferase
Query= SwissProt::P07871 (424 letters) >NCBI__GCF_000527155.1:WP_051463071.1 Length = 392 Score = 235 bits (600), Expect = 2e-66 Identities = 141/391 (36%), Positives = 223/391 (57%), Gaps = 12/391 (3%) Query: 37 DVVVVHGRRTPIGRAGRGGFKDTTPDELLSAVLTAVLQ-DVKLKPECLGDISVGNVLQPG 95 DVV V G RTP G+AG+ + +T D+++ + ++L+ + L PE + ++++ Q G Sbjct: 3 DVVFVDGVRTPFGKAGKM-YDETRADDMIIRCIRSLLERNPSLPPEKIDEVALAATTQTG 61 Query: 96 -AGAAMARIAQFLSGIPETVPLSAVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 G M R A L+G+P+TVP +++R C+ + AV A I + +YD+ +A GVESM+ Sbjct: 62 DQGLTMGRTASLLAGLPKTVPGFSIDRMCAGAMTAVTTTASAIASRNYDLVIAGGVESMS 121 Query: 155 LSERGNPGNISSRLLENEKARDCLIPMGITSENVAERFG-ISRQKQDAFALASQQKAASA 213 G + + R++ + + MG T+EN+ + + I++ + DA+A +Q +A A Sbjct: 122 NHPMGEGADPNPRIIAEKLVDPEALQMGKTAENIHDLYPEITKDRADAYA--AQTQARYA 179 Query: 214 QSKGCFRAEIVPVTTTVLDDKGDRKTITVSQDEGVRPSTTMEGLAKLKPAFKDGGSTTAG 273 + + +IV ++ + + DE RP TT+EGLA+LK F+ G TAG Sbjct: 180 EHVKQLQNDIVSMSAY----SSEEGWTVANGDEPPRPGTTVEGLAELKTPFRPYGRVTAG 235 Query: 274 NSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPAALQKAG 333 NS+ ++DGA A +L A ++GL + YA GV P++MGIGP A AL KAG Sbjct: 236 NSAPLTDGATACVLTDSETASDMGLSAAMKMVGYAFSGVDPEVMGIGPVPATEKALAKAG 295 Query: 334 LTVNDIDIFEINEAFASQALYCVE--KLGIPAEKVNPLGGAIALGHPLGCTGARQVVTLL 391 L+++DI +FEINEAFA Q L ++ K+ +VNP GGAIA+GHPL +G R + L Sbjct: 296 LSIDDIGLFEINEAFAVQVLAFLDHFKISETDPRVNPWGGAIAVGHPLASSGVRLMTQLA 355 Query: 392 NELKRRGRRAYGVVSMCIGTGMGAAAVFEYP 422 + R YG+ +MC+G G G ++E P Sbjct: 356 RQFAERPDVRYGITTMCVGIGQGGTVIWENP 386 Lambda K H 0.316 0.133 0.378 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: 414 Number of extensions: 21 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: 392 Length adjustment: 31 Effective length of query: 393 Effective length of database: 361 Effective search space: 141873 Effective search space used: 141873 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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