Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate YP_002825570.1 NGR_c10280 O-acetylhomoserine aminocarboxypropyltransferase
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000018545.1:YP_002825570.1 Length = 427 Score = 475 bits (1222), Expect = e-138 Identities = 234/427 (54%), Positives = 309/427 (72%), Gaps = 10/427 (2%) Query: 17 TIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTDVLE 76 T+A+H G +PDPTT +RA P+YQTTS+VF D DHAA LFGLQ+FGNIY+R+MNPT VLE Sbjct: 10 TLAVHAGAQPDPTTGARATPIYQTTSFVFNDADHAAALFGLQQFGNIYSRIMNPTQAVLE 69 Query: 77 KRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKLGIK 136 +R+AALEGG AALATASG +A++L I+ G VA+ LYGG+ N F + Sbjct: 70 ERIAALEGGTAALATASGHAAQLLVFHTIMGPGDNFVAARQLYGGSVNQFGQAFKSFDWQ 129 Query: 137 VHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNTMPS 196 V + D +DPE+F + +T+A + E+L NP +DIAA+++VA+ G+PL++DNTM + Sbjct: 130 VRWADCADPESFETQIDARTKAIFVESLANPGGIFVDIAAIAEVARRHGLPLIVDNTMAT 189 Query: 197 PYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWG-NGKFKNFTEPDPSYHGL 255 PYLV PL+HGADIVVHSLTKF+GGHG S+GGII+DGG+F+W +GK+ +EP P Y G+ Sbjct: 190 PYLVRPLEHGADIVVHSLTKFIGGHGNSMGGIIVDGGTFDWSKSGKYPLLSEPRPEYGGV 249 Query: 256 KFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHSGN 315 + FG N AF + ARV GLRD GPAISPFNA+ I GVETLPLRM+RH N Sbjct: 250 VLHQAFG--------NFAFAIAARVLGLRDFGPAISPFNAFLIQTGVETLPLRMQRHCDN 301 Query: 316 ALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKFID 375 AL VA +L+ ++ W+ Y GL D N+A K+Y +G GA+ F + GG E K+F++ Sbjct: 302 ALAVARWLKGRDEVSWIRYAGLEDDPNHALQKRYSPKGA-GAVFTFGLSGGYEAGKRFVE 360 Query: 376 GLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILVDL 435 GLE+FS LANIGD +SL IHPASTTH+QLT +Q++AG P VRLS+G+E++DDI+ DL Sbjct: 361 GLEMFSHLANIGDTRSLVIHPASTTHRQLTPEQQVAAGAGPDVVRLSIGIEDVDDIIADL 420 Query: 436 EEALKNI 442 E+AL +I Sbjct: 421 EQALASI 427 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: 601 Number of extensions: 29 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: 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