Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_086508403.1 BZY95_RS02365 acetyl-CoA C-acyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982 (397 letters) >NCBI__GCF_002151265.1:WP_086508403.1 Length = 395 Score = 464 bits (1195), Expect = e-135 Identities = 232/387 (59%), Positives = 296/387 (76%), Gaps = 1/387 (0%) Query: 8 IVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLPAGLGQ 67 IV +SA RTPMGG G L SLTAP+L A AI+AA+ERAG+ + S+DE + GCVLP G+ Q Sbjct: 7 IVFLSATRTPMGGMLGSLASLTAPELAATAIRAAIERAGIEAGSIDEGIMGCVLPGGVKQ 66 Query: 68 APARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPY 127 PARQA AG+ TT+NK+CGSGM+AA+LAHD++ AGS +V++AGGMESMSNAP+ Sbjct: 67 GPARQAMRQAGIPDGIGATTINKLCGSGMKAAMLAHDLIRAGSGEVILAGGMESMSNAPH 126 Query: 128 LLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQDAFAIAS 187 +L +AR GYR+GHG ++D MFLDGLEDA + G+LMG FA+D A G+SRE D FAIAS Sbjct: 127 VLTKARTGYRLGHGELKDHMFLDGLEDA-ETGKLMGVFAQDIASQRGYSRERLDDFAIAS 185 Query: 188 TTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFREGGTVTA 247 RA A G AE+ P+TVT + + V+ +DEQP +A+LDKI L+PAF + GT+TA Sbjct: 186 LERAMAATNAGHLAAEMAPVTVTSRQGESVVEHDEQPFQAKLDKIRQLRPAFAKDGTITA 245 Query: 248 ANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIKKLMKKT 307 ANSSSISDGA+AL+L QS A + G KPLA + GH+ + P F +AP+GAI KLMKK Sbjct: 246 ANSSSISDGASALILASQSAADRLGSKPLARMLGHSTHSQHPSEFTIAPVGAIDKLMKKL 305 Query: 308 GWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARILVTLLS 367 GW + DVDL E+NEAFAVV + AM L+IPH+K+NV GGACA GHPIG++G+RI+ TL+ Sbjct: 306 GWGVADVDLFEINEAFAVVTLLAMDGLDIPHDKVNVFGGACAQGHPIGSTGSRIIATLIH 365 Query: 368 ALRQKGLKRGVAAICIGGGEATAMAVE 394 ALR KG KRG+A++CIGGGEATA+A+E Sbjct: 366 ALRTKGGKRGIASLCIGGGEATAVAIE 392 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: 536 Number of extensions: 25 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: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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 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