Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_034993560.1 DL88_RS06485 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000745425.1:WP_034993560.1 Length = 427 Score = 444 bits (1143), Expect = e-129 Identities = 225/424 (53%), Positives = 295/424 (69%), Gaps = 10/424 (2%) Query: 17 TIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTDVLE 76 T+A+H G PDPTT +RA P+YQTTSYVF + D AA FGLQEFGNIYTR+ NPT VLE Sbjct: 11 TLAVHAGAAPDPTTGARATPIYQTTSYVFANADQAAARFGLQEFGNIYTRITNPTNAVLE 70 Query: 77 KRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKLGIK 136 +R+AALEGG AALA ASG +A++L N+++ G I+A++ LYGGT N L ++F G Sbjct: 71 ERIAALEGGTAALAVASGHAAQLLVFHNLMQPGDTILAATKLYGGTVNQLSHSFKNFGWN 130 Query: 137 VHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNTMPS 196 V+F D D E F A +T+A + E++ NP D+ AV+KVAK +PL++DNT+ S Sbjct: 131 VNFADTDDIEAFAAAVTPQTKAIFVESIANPGGTITDLEAVAKVAKAHKIPLIVDNTLAS 190 Query: 197 PYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNW-GNGKFKNFTEPDPSYHGL 255 PYL+ P +HGADI+VHS TKFLGG G S+GG+I+DGG+F+W G+ ++ EP Y GL Sbjct: 191 PYLIRPFEHGADIIVHSATKFLGGQGNSMGGLIVDGGTFDWRGDKRYPMLCEPHAEYGGL 250 Query: 256 KFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHSGN 315 + F F AF L AR LRDLGP++SPFNA+ +L G+ETLPLRM+RH N Sbjct: 251 IIADTFPHF--------AFALAARALSLRDLGPSLSPFNAFLLLNGIETLPLRMQRHCDN 302 Query: 316 ALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKFID 375 AL VA L +H +EWV+Y GL D+ YA AKKY G GA+ F IK G E A + + Sbjct: 303 ALLVATHLAQHRAVEWVSYAGLPEDRYYALAKKYTPLGA-GAVFTFGIKDGYEAALRTVS 361 Query: 376 GLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILVDL 435 L+LFSLLAN+GD +SL IHPASTTH+QLT ++I+AG P +RLS+G+E+ DI+ DL Sbjct: 362 KLKLFSLLANVGDTRSLVIHPASTTHRQLTDAQKIAAGAGPEVIRLSIGIEDPRDIIADL 421 Query: 436 EEAL 439 ++AL Sbjct: 422 DQAL 425 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: 533 Number of extensions: 17 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