Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_025273660.1 HALAL_RS0108855 acetyl-CoA C-acyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_000527155.1:WP_025273660.1 Length = 387 Score = 314 bits (805), Expect = 2e-90 Identities = 175/386 (45%), Positives = 255/386 (66%), Gaps = 10/386 (2%) Query: 5 VIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAGLGQN 64 VI +A RT IG + L D A LG AIK A++++ ++P+ V +VILG+VL AG GQN Sbjct: 8 VILAAARTPIGRFTGGLADFSAPALGGVAIKAALERSNVQPDQVGQVILGHVLPAGSGQN 67 Query: 65 PARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSRAPYL 124 PARQA+ G+P+ +P++++NKVC SG+ + +A + +++GD D I+ GGME+M++AP++ Sbjct: 68 PARQAAVAGGIPMSVPSLSVNKVCLSGMTAIGIADRFLRSGDDDFIVVGGMESMTQAPHM 127 Query: 125 ANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFALASQK 184 +R GY+ G+ +D + DGL DA++ MG + E ++ ISR++QD +A SQ+ Sbjct: 128 LPKSRRGYKYGDVTMLDHLAFDGLTDAYDGISMGESTERHVQKTGISRQDQDGYAAESQQ 187 Query: 185 KAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGTVTAG 244 +A +A + +EIVPV + RKG VD DE PR +T EGLA L+PAF KDGT+T G Sbjct: 188 RAAKAASAR--AEEIVPV--ETRKG--TVDADESPRGDTTAEGLAGLRPAFAKDGTITPG 241 Query: 245 NASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGS-AGVDPAIMGYGPFYATKAAIEKA 303 +S +ND A LV+ + KA+ELG++ ++I+SY + AG D +++ P A KAA+ Sbjct: 242 TSSPMNDGAVALVLTTKSKAEELGLEWESEILSYSTVAGPDNSLLRQ-PSNAIKAALRDT 300 Query: 304 GWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVTLVH 363 G+ D+L+ +E NEAFAA +LA DL D VN +GGAIALGHP+GASGAR++ TL Sbjct: 301 GYGADDLEAVEINEAFAAVALASIDDLGVDPAHVNRDGGAIALGHPLGASGARLVQTL-- 358 Query: 364 AMQKRDAKKGLATLCIGGGQGTAILL 389 + Q G A LC GGGQG I+L Sbjct: 359 SRQLSSGAVGAAGLCGGGGQGDGIIL 384 Lambda K H 0.315 0.132 0.375 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: 427 Number of extensions: 20 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: 392 Length of database: 387 Length adjustment: 30 Effective length of query: 362 Effective length of database: 357 Effective search space: 129234 Effective search space used: 129234 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 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