Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_013644806.1 METBO_RS06070 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000191585.1:WP_013644806.1 Length = 439 Score = 531 bits (1368), Expect = e-155 Identities = 261/427 (61%), Positives = 326/427 (76%), Gaps = 5/427 (1%) Query: 17 TIALHGGQE-PDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTDVL 75 TI LH GQE PD T SRAVP+Y T+SYVF DT+HAA LFGL+EFGNIYTR+MNPTTDV Sbjct: 17 TIGLHVGQEEPDSATGSRAVPIYLTSSYVFNDTEHAANLFGLREFGNIYTRIMNPTTDVF 76 Query: 76 EKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKLGI 135 EKRVAA+EGG AL ASG SA LA+LN+ E G+ IV+ +LYGGTY L +YT P+LG Sbjct: 77 EKRVAAVEGGATALGVASGMSAIFLAVLNVSELGENIVSGDNLYGGTYELFNYTLPRLGR 136 Query: 136 KVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNTMP 195 V FV+ PE F A ++KTRA Y E+LGNPKLD D ++K+A + +PL++DNT Sbjct: 137 TVKFVNSEKPEEFEAAIDEKTRAIYVESLGNPKLDVPDFEKLAKIAHDHDIPLIVDNT-S 195 Query: 196 SPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGKFKNFTEPDPSYHGL 255 + L+ P+ +GADI V S TK++GGHGTSIGG+I+D G FNWGNGKF FT+PDPSYHGL Sbjct: 196 TVGLLRPIDYGADITVISATKYIGGHGTSIGGVIVDSGKFNWGNGKFPQFTDPDPSYHGL 255 Query: 256 KFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHSGN 315 K+WE FG F G NIAF ++ARV LRDLGPA+SPFNA+Q LQG+ETL LR+ +H+ N Sbjct: 256 KYWETFGDFP--GAGNIAFTIRARVVLLRDLGPALSPFNAFQFLQGLETLELRVLKHAEN 313 Query: 316 ALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKFID 375 ALKVA+ L+ HPK+ W+NYPGL D + A KY + G +G ++GF I+GG+E KKFI+ Sbjct: 314 ALKVAKHLKNHPKVSWINYPGLEEDPRHEVASKYLKGG-YGGLIGFGIEGGLESGKKFIE 372 Query: 376 GLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILVDL 435 +ELFS LANIGD+KSL IHPASTTHQQLT EQ + GVT FVRLS+GLE+++DI+ D+ Sbjct: 373 NVELFSHLANIGDSKSLVIHPASTTHQQLTREEQETTGVTEDFVRLSIGLEDVEDIIADI 432 Query: 436 EEALKNI 442 ++AL I Sbjct: 433 DQALSKI 439 Lambda K H 0.317 0.137 0.402 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: 610 Number of extensions: 25 Number of successful extensions: 4 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: 442 Length of database: 439 Length adjustment: 32 Effective length of query: 410 Effective length of database: 407 Effective search space: 166870 Effective search space used: 166870 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: 51 (24.3 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