Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate YP_427033.1 Rru_A1946 acetyl-CoA acetyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982 (397 letters) >NCBI__GCF_000013085.1:YP_427033.1 Length = 406 Score = 491 bits (1265), Expect = e-143 Identities = 253/391 (64%), Positives = 303/391 (77%) Query: 4 SNDPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLPA 63 + DP+VIV A RTP+G F G L SL AP+LGA AI A++ A VD V+ GCVLPA Sbjct: 13 AGDPVVIVGAKRTPLGAFMGSLGSLRAPELGARAISGALDGLEGAEHRVDGVIMGCVLPA 72 Query: 64 GLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMS 123 G GQAPARQAA AGL + C T+NKMCGSGMEAAILA + L AG+A+V+VAGGMESM+ Sbjct: 73 GQGQAPARQAAHAAGLSWAVPCATVNKMCGSGMEAAILACNTLAAGAAEVMVAGGMESMT 132 Query: 124 NAPYLLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQDAF 183 NAPYLLD+AR G+R+GHG+V D MFLDGLEDAYD+GRLMGTFAED A++ FSRE QDAF Sbjct: 133 NAPYLLDKARGGHRLGHGQVVDHMFLDGLEDAYDRGRLMGTFAEDTAQSYRFSREEQDAF 192 Query: 184 AIASTTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFREGG 243 A+ S RA++AI DG E V + V E ++ DE P KA D+I LKPAFREGG Sbjct: 193 ALESLLRAKRAIADGVMARECVSVVVRERGEDHLVETDEAPIKANPDRIPHLKPAFREGG 252 Query: 244 TVTAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIKKL 303 TVTAANSSSISDGAAALVL R S A + G +PLAV+ GHAA+A P LFP AP+GAI+++ Sbjct: 253 TVTAANSSSISDGAAALVLTRASVADRAGWRPLAVVRGHAAYAAEPELFPTAPVGAIERM 312 Query: 304 MKKTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARILV 363 + + GW ++VDL E+NEAFAVV + A+ L + +LNVHGGACALGHPIGASGARI+V Sbjct: 313 LARVGWRRDEVDLWEINEAFAVVALVALRDLGLDPGRLNVHGGACALGHPIGASGARIIV 372 Query: 364 TLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 TLL+ALRQ+GL RGVA++CIGGGEATAMAVE Sbjct: 373 TLLNALRQRGLTRGVASLCIGGGEATAMAVE 403 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: 558 Number of extensions: 20 Number of successful extensions: 1 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: 406 Length adjustment: 31 Effective length of query: 366 Effective length of database: 375 Effective search space: 137250 Effective search space used: 137250 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