Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_011842744.1 RSPH17029_RS19805 acetyl-CoA C-acyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982 (397 letters) >NCBI__GCF_000015985.1:WP_011842744.1 Length = 386 Score = 517 bits (1332), Expect = e-151 Identities = 263/392 (67%), Positives = 313/392 (79%), Gaps = 8/392 (2%) Query: 3 MSNDPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLP 62 M+ +PIVI A RTPMG FQG LK T +LG+AAI AA+ RAG+A ++V+EV+ GCVLP Sbjct: 1 MAAEPIVIAGAARTPMGAFQGALKGRTGVELGSAAISAALARAGLAPEAVEEVVMGCVLP 60 Query: 63 AGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESM 122 AGLGQAPARQAALGAGL S C TLNK+CGSGM+AA+ AHDM+ AGSA +VVAGGMESM Sbjct: 61 AGLGQAPARQAALGAGLPLSVPCATLNKVCGSGMKAAMAAHDMIRAGSAGIVVAGGMESM 120 Query: 123 SNAPYLLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQDA 182 SNAPYLLD+AR GYR+GHGRV D MFLDGLEDAYD+GR MGTFAEDCAE F+R+AQDA Sbjct: 121 SNAPYLLDKARGGYRIGHGRVLDHMFLDGLEDAYDRGRAMGTFAEDCAEAYQFTRDAQDA 180 Query: 183 FAIASTTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFREG 242 +A+AS RAQ AI +G F AE+V + ++ DE P +AR +KI L+PAFREG Sbjct: 181 YALASLARAQAAIAEGRFAAEVVAVD--------GVAVDEAPGRARPEKIPQLRPAFREG 232 Query: 243 GTVTAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIKK 302 GTVTAANSSSISDGAAALV+ A+ QGL PLA I GHA+ A P LF API AI K Sbjct: 233 GTVTAANSSSISDGAAALVIASAGAAEAQGLTPLATIRGHASHAQAPNLFTTAPIFAIGK 292 Query: 303 LMKKTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARIL 362 L+++ GWS +VDL E+NEAFAVV MAAM L++PH+K+NV+GGACALGHPIG SGARI+ Sbjct: 293 LLERVGWSAAEVDLFEINEAFAVVAMAAMRDLDLPHDKVNVNGGACALGHPIGCSGARIV 352 Query: 363 VTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 VTL+ ALR +GL+RGVA++CIGGGEATA+AVE Sbjct: 353 VTLIEALRARGLRRGVASLCIGGGEATALAVE 384 Lambda K H 0.318 0.132 0.376 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: 566 Number of extensions: 22 Number of successful extensions: 2 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: 397 Length of database: 386 Length adjustment: 31 Effective length of query: 366 Effective length of database: 355 Effective search space: 129930 Effective search space used: 129930 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 Apr 10 2024. 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