Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_028586001.1 G494_RS0120435 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000429965.1:WP_028586001.1 Length = 427 Score = 483 bits (1242), Expect = e-141 Identities = 242/423 (57%), Positives = 306/423 (72%), Gaps = 10/423 (2%) Query: 17 TIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTDVLE 76 T LH GQ DP T SRAVP+YQTTSY FKD+ HAA LF L+E GNIYTR+MNPTTDVLE Sbjct: 12 TRQLHAGQVADPATGSRAVPIYQTTSYAFKDSQHAADLFALKEAGNIYTRIMNPTTDVLE 71 Query: 77 KRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKLGIK 136 +R+A LEGGV ALA +SG A+++A L I G IV+S+SLYGGTY L YT P+LGI Sbjct: 72 QRLADLEGGVGALAASSGHGAQVMAFLTICGQGDHIVSSNSLYGGTYTQLQYTLPRLGIT 131 Query: 137 VHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNTMPS 196 V F D DPE+F +A T+ Y ETLGNP L V+ +A V +PLVIDNT+ + Sbjct: 132 VSFADPRDPESFARAIQPNTKLIYGETLGNPALTVFPFEEVAAIAAAVQIPLVIDNTLAT 191 Query: 197 PYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGKFKNFTEPDPSYHGLK 256 PYL PL+ GA+IV HS TKFL GHG SIGGI++DGG+F+W +GK +FTEPDPSYHGL Sbjct: 192 PYLCRPLEWGANIVSHSTTKFLNGHGNSIGGILVDGGNFDWQSGKISSFTEPDPSYHGLI 251 Query: 257 FWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHSGNA 316 + E+ AFILKARVQ LRD+G + +PFN+W +QG+ETL LRMERH NA Sbjct: 252 YAELGAP---------AFILKARVQVLRDIGVSQAPFNSWLTVQGIETLSLRMERHVANA 302 Query: 317 LKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKFIDG 376 L+ A FL+ H ++ WV+YPGLS+ ++ A +Y +G GA++ F I+GGVE ++FID Sbjct: 303 LETARFLEGHARVSWVSYPGLSSHPDHGRACRYLPQGA-GAVIAFGIQGGVEAGRRFIDH 361 Query: 377 LELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILVDLE 436 L+LFS +AN+GDAKSLAIHPASTTH QL+ E + AGV +RLS+GLE+++DI DL+ Sbjct: 362 LQLFSHVANVGDAKSLAIHPASTTHSQLSPAELLEAGVQEEMIRLSIGLEDLEDIFWDLD 421 Query: 437 EAL 439 +AL Sbjct: 422 QAL 424 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: 558 Number of extensions: 16 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: 442 Length of database: 427 Length adjustment: 32 Effective length of query: 410 Effective length of database: 395 Effective search space: 161950 Effective search space used: 161950 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