Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate WP_085772529.1 B1812_RS16320 acetyl-CoA C-acyltransferase
Query= reanno::pseudo3_N2E3:AO353_25685 (397 letters) >NCBI__GCF_002117405.1:WP_085772529.1 Length = 396 Score = 506 bits (1303), Expect = e-148 Identities = 256/391 (65%), Positives = 308/391 (78%) Query: 4 SHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSA 63 S +VIV A RTP+G F GELK +AP+LGA AI A+ R+ + A+ ++EV GCVL+A Sbjct: 3 SSGSVVIVGAARTPIGAFLGELKEATAPELGACAIAGALIRSKIPAERIDEVCMGCVLTA 62 Query: 64 GLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMS 123 GLGQAPARQAAL AGL ST C T+NKMCGSGM+A +LAHD L AGSA +VAGGMESMS Sbjct: 63 GLGQAPARQAALEAGLPDSTGCVTVNKMCGSGMKAIMLAHDALSAGSAGAIVAGGMESMS 122 Query: 124 NAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEF 183 NAPYLL RAR+GYRMGHGK+LDHMFLDGLEDAY+KGRLMG+FAEDCA A FTR QDE+ Sbjct: 123 NAPYLLARARAGYRMGHGKILDHMFLDGLEDAYEKGRLMGSFAEDCARAYQFTRREQDEY 182 Query: 184 AIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGG 243 AIAS RAQQA +G+F+++IVP+++ KE + I DE P KA L++I LKPAF G Sbjct: 183 AIASLMRAQQAATEGAFDSQIVPMRIAGRKETRTIDVDETPRKANLEEIPRLKPAFAPDG 242 Query: 244 TVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKL 303 ++TAAN+SSISDGAAAL+L + A GL PLA + GHA A P FP AP+GAI+KL Sbjct: 243 SITAANASSISDGAAALVLTTEAAARSGGLIPLATVVGHATHAAAPRDFPTAPIGAIEKL 302 Query: 304 LKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILV 363 L + GW+ DEV+LFE+NEAFAVV + M L + H+KVNVHGGACALGHPIGASGARI+V Sbjct: 303 LSRIGWTRDEVDLFEINEAFAVVVMAAMHDLGLSHAKVNVHGGACALGHPIGASGARIVV 362 Query: 364 TLLSALRQKGLKRGVAAICIGGGEATAMAVE 394 TLL AL + GL+RGVAA+CIGGGEATA+A+E Sbjct: 363 TLLYALERYGLRRGVAALCIGGGEATALAIE 393 Lambda K H 0.318 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: 492 Number of extensions: 9 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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 09 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