Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_012756940.1 RLEG_RS06535 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000023185.1:WP_012756940.1 Length = 427 Score = 483 bits (1242), Expect = e-141 Identities = 235/427 (55%), Positives = 309/427 (72%), Gaps = 10/427 (2%) Query: 17 TIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTDVLE 76 T+A+H G +PDPTT +R P+YQTT++VF D+DHAA LFGLQ FGNIYTR+MNPT VLE Sbjct: 10 TLAIHAGAQPDPTTGARVTPIYQTTAFVFNDSDHAAALFGLQAFGNIYTRIMNPTQAVLE 69 Query: 77 KRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKLGIK 136 +RVAALEGG AALA ASG +A+++ NI+ G+ +A+ LYGG+ N + F G + Sbjct: 70 ERVAALEGGTAALAVASGHAAQVIVFHNIMRPGENFIAARQLYGGSINQFGHAFENFGWQ 129 Query: 137 VHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNTMPS 196 V + D +DP +F +DKTR + E+L NP +DIAA++ VA G+PL++DNTM + Sbjct: 130 VRWADAADPASFESQIDDKTRGIFIESLANPGGTFVDIAAIADVAHRHGLPLIVDNTMAT 189 Query: 197 PYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWG-NGKFKNFTEPDPSYHGL 255 PY + P++HGADIVVHSLTKFLGGHG S+GG+I+DGG+F+W +G + + P P Y+G+ Sbjct: 190 PYFIRPIEHGADIVVHSLTKFLGGHGNSMGGLIVDGGTFDWSKSGNYPMLSSPRPEYNGM 249 Query: 256 KFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHSGN 315 FG N AF + ARV GLRDLGPAISPFNA+ IL G+ETLPLRM+RHS N Sbjct: 250 VLHATFG--------NFAFAIAARVLGLRDLGPAISPFNAFLILTGIETLPLRMQRHSDN 301 Query: 316 ALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKFID 375 A+ VA++L+ H KI WVNY GL D N+A ++Y +G G++ F +KGG E K ++ Sbjct: 302 AIAVAKWLKAHSKIAWVNYAGLDDDPNHALQQRYSPKGA-GSVFTFGVKGGYEAGKTLVE 360 Query: 376 GLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILVDL 435 GLELFS LANIGD +SL IHPASTTH+QLT ++I+AG PG VRLSVG+E++ DI+ DL Sbjct: 361 GLELFSHLANIGDTRSLVIHPASTTHRQLTDEQRIAAGAGPGVVRLSVGIEDVKDIIADL 420 Query: 436 EEALKNI 442 E+AL I Sbjct: 421 EQALSKI 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: 589 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: 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