Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate GFF401 PGA1_c04120 3-ketoacyl-CoA thiolase FadA
Query= SwissProt::O32177 (391 letters) >FitnessBrowser__Phaeo:GFF401 Length = 391 Score = 330 bits (846), Expect = 4e-95 Identities = 188/392 (47%), Positives = 246/392 (62%), Gaps = 4/392 (1%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60 MK+AVIVS ART + K+ +GS LG V ++RA G I+D IIGC PE Sbjct: 1 MKQAVIVSAARTGLAKSFRGSFNQTHGATLGGHAVAAAVERASLEGGVIEDCIIGCGFPE 60 Query: 61 AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120 G N+ R I AGLP T +TVNR+C+SGLQ+IA AA++I +AGG ES+ Sbjct: 61 GATGHNIGRQIALRAGLPQTAAGMTVNRFCASGLQTIALAAQQITAEGAGPMVAGGVESI 120 Query: 121 SQV-PMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179 S V P + V P L E P+ YM+M TA+ VA++YG+SRE QDA+ +RS Q A A Sbjct: 121 SMVQPNVTQVQDP--WLQEHNPDVYMAMIDTADVVAERYGISREAQDAYGLRSQQKIAAA 178 Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPME-KQFVFSQDEGVRPQTTADILSTLRPAFSVDG 238 G F DEIVP++ + D + ++ ++DE RPQTT D L+ L P Sbjct: 179 QDAGIFDDEIVPMQTVMAVKDRDTGEISHREVTVNRDECNRPQTTLDGLAGLEPVRGAGK 238 Query: 239 TVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRA 298 +TAGN+SQ SDGAAAV++M+ ++A GL P+ FR F V G P+ MGIGPV A+PR Sbjct: 239 FITAGNASQLSDGAAAVVMMEADEASRRGLDPMGAFRGFCVAGCAPDEMGIGPVHAVPRL 298 Query: 299 LKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTL 358 L+ G+ + DI L+ELNEAFASQA+ LGI +E NVNGG+IA+GHP G TG ++ Sbjct: 299 LERHGVTVADIDLWELNEAFASQALFCRDNLGIPDEICNVNGGSIAIGHPFGMTGARMVG 358 Query: 359 SLIHEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390 L+ E RR + GVVTMCIGGGMGAAG+FE+ Sbjct: 359 HLLREGHRRGAKLGVVTMCIGGGMGAAGLFEI 390 Lambda K H 0.316 0.133 0.377 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: 446 Number of extensions: 13 Number of successful extensions: 3 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: 391 Length of database: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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 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