Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate YP_004143587.1 Mesci_4427 O-acetylhomoserine/O-acetylserine sulfhydrylase
Query= BRENDA::P94890 (442 letters) >NCBI__GCF_000185905.1:YP_004143587.1 Length = 426 Score = 471 bits (1211), Expect = e-137 Identities = 231/427 (54%), Positives = 306/427 (71%), Gaps = 10/427 (2%) Query: 17 TIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTDVLE 76 T+A+H G +PDP T +RA P+YQTTS+VF D DHAA LFGL+ FGNIYTR+MNPT VLE Sbjct: 9 TLAVHAGAKPDPATGARATPIYQTTSFVFDDADHAASLFGLKAFGNIYTRIMNPTQAVLE 68 Query: 77 KRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKLGIK 136 +R+AALEGG AALA ASG +A+++ N+++ G VA++ LYGG+ N + F G + Sbjct: 69 ERMAALEGGTAALAVASGHAAQVIVFHNLMQPGDNFVAANKLYGGSINQFGHAFKNYGWE 128 Query: 137 VHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNTMPS 196 V + D +D F +D+T+A + E+L NP +DI + +A++ G+PL++DNT+ S Sbjct: 129 VRWADTNDISTFESQIDDRTKAIFIESLANPGGTFVDIEKIGDIARKHGLPLIVDNTLAS 188 Query: 197 PYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWG-NGKFKNFTEPDPSYHGL 255 PYL+ P++HGADIVVHSLTKF+GGHG SIGG I+DGG+F+W +GK+ +EP P Y GL Sbjct: 189 PYLIRPIEHGADIVVHSLTKFIGGHGNSIGGAIVDGGTFDWSKSGKYPMLSEPRPEYGGL 248 Query: 256 KFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHSGN 315 E FG N AF + ARV GLRDLGPAISPFNA+ IL G+ETLPLRM+RH N Sbjct: 249 VLHETFG--------NFAFAIAARVLGLRDLGPAISPFNAFLILTGLETLPLRMQRHCDN 300 Query: 316 ALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKFID 375 A+ VA +L HPK+ VNYPGL +DKN A KKY G GA+ F +KGG + KF++ Sbjct: 301 AVTVAAWLSNHPKVASVNYPGLPSDKNNALQKKYSPFGA-GAVFTFALKGGYDAGVKFVE 359 Query: 376 GLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILVDL 435 LELFS LAN+GD KSL IHPASTTH+QL+ +++ AG P VRLS+G+E+++DI+ DL Sbjct: 360 ALELFSHLANVGDTKSLVIHPASTTHRQLSDEQKVKAGAGPDTVRLSIGIEDVNDIVADL 419 Query: 436 EEALKNI 442 E+AL + Sbjct: 420 EQALAKV 426 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: 21 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: 426 Length adjustment: 32 Effective length of query: 410 Effective length of database: 394 Effective search space: 161540 Effective search space used: 161540 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