Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_011307393.1 MBAR_RS12890 homoserine O-acetyltransferase
Query= BRENDA::I1R9N5 (509 letters) >NCBI__GCF_000195895.1:WP_011307393.1 Length = 579 Score = 224 bits (572), Expect = 5e-63 Identities = 150/440 (34%), Positives = 212/440 (48%), Gaps = 31/440 (7%) Query: 89 TLNYHHKEPFLLDWGGILPEFNIAYETWGELNADKSNAILLHTGLSASSHAHSTET-NPK 147 ++NY F L+ G L I YE +G++NADKSN IL+ L+ +HA T + K Sbjct: 27 SMNYEIPGIFRLESGKTLSHVRIEYEMYGKMNADKSNVILVCHALTGDAHAAGFHTGDKK 86 Query: 148 PGWWEKFIGPGGPLDTNKYHVICTNVIGGCNGSTGPSSVDPGNGERYATRFPILTMDDMV 207 PGWW IGP DT +Y ++C+N+IGGC GSTGPSS++P G+ Y FPILT+ DMV Sbjct: 87 PGWWNIVIGPNKAFDTERYCIVCSNIIGGCKGSTGPSSINPETGKPYGISFPILTIADMV 146 Query: 208 RAQFKLLDHLGIDKLYASVGSSMGGMQSLAAGVQSPSRVGRIVSISGCARSHPYSIAMRH 267 AQ KL++HLG+ +L+A G SMGGMQ L V P V + ++I+ A + P IA Sbjct: 147 NAQKKLVEHLGVKQLFAVAGGSMGGMQVLQWTVSYPEMVKKAIAIATTASTTPQQIAFGA 206 Query: 268 TQRQVLMMDPNWNRGFYYGKVPPHAGMKLAREIATVTYRSGPEWEQRFGRRRADSSKP-- 325 R+ + DP WN G YYGK P G+ LAR I +TY S +++FGR + + P Sbjct: 207 IGRKAITDDPKWNGGNYYGKKTPAQGLALARMIGHITYLSDASMQKKFGRDKQEKVGPDM 266 Query: 326 PALCPDFLIETYLDHAGEKWCLNYDPNSLLYVSKAMDLFDLGIEHQRATHARRQDREKKL 385 P + E A K P + S E T ++ + Sbjct: 267 PKISSKVSSEV-SPAASSKTSSETSPETSSKTSS-----KTSSETSSKTSSKTSSKTSSK 320 Query: 386 ASGEASPLSSDAACSLTLPNKPYEEQPGSHPDPS--------DPNVVPGSRPPED----- 432 S E S +S S T P++ Q S+ + D N D Sbjct: 321 TSSETSSETSSKTFSETFPDRSSHFQVESYLNHQGDTFTKRFDANSYLYITKAVDFFDLS 380 Query: 433 ----LIHGLTPLRDTPTLVMGVASDILFPAWQQREVAEAIRLAGNRNVTHVELSEEMSMF 488 LI GL+ + LV+ + SD L+P +Q +E+ A+ N + E S + Sbjct: 381 KNGSLIEGLSVV-TAKYLVISITSDWLYPPYQSQEIVSAL----TANGVDAKYEEIRSQY 435 Query: 489 GHDTFLLDLKYIGNNLRMFL 508 GHD FLL+ + +R FL Sbjct: 436 GHDAFLLEEGQLNYLIRGFL 455 Lambda K H 0.317 0.134 0.413 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: 620 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 509 Length of database: 579 Length adjustment: 35 Effective length of query: 474 Effective length of database: 544 Effective search space: 257856 Effective search space used: 257856 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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