Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate Dsui_2039 Dsui_2039 OAH/OAS sulfhydrylase
Query= BRENDA::P94890 (442 letters) >FitnessBrowser__PS:Dsui_2039 Length = 428 Score = 501 bits (1291), Expect = e-146 Identities = 245/424 (57%), Positives = 309/424 (72%), Gaps = 9/424 (2%) Query: 16 ETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTDVL 75 +T++LH GQ PD T SRA P+YQT +YVF +HAA LF LQ FGN+Y+RL NPT VL Sbjct: 9 DTLSLHAGQVPDAATGSRATPIYQTAAYVFDSPEHAASLFNLQTFGNVYSRLSNPTVAVL 68 Query: 76 EKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKLGI 135 E+R+AALEGG AA+A ASG +A+M+ALLN+ EAG EIVA+ +LYGGT+ L F KLGI Sbjct: 69 EERIAALEGGKAAVAVASGMAAQMVALLNLCEAGDEIVAARTLYGGTHTQLDVNFRKLGI 128 Query: 136 KVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNTMP 195 FVD DPENF KA +T+ YAET+GNP L+ LDI AV+++A G+PL +DNT Sbjct: 129 NTIFVDSDDPENFAKAITPRTKVIYAETMGNPGLNVLDIEAVARIANAAGLPLFVDNTFA 188 Query: 196 SPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGKFKNFTEPDPSYHGL 255 SPYL P + GA IVVHS TKF+GGHGT++GGII++ G F W NGKF TEP P YHG+ Sbjct: 189 SPYLCRPFEWGAAIVVHSATKFIGGHGTTLGGIIVESGKFPWDNGKFATMTEPSPGYHGV 248 Query: 256 KFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHSGN 315 KF+E FG N F K R++GLR GPA+SPFNA+ +LQGVETL LRM+RH N Sbjct: 249 KFYETFG--------NFGFTAKCRMEGLRTFGPALSPFNAFLLLQGVETLSLRMDRHCSN 300 Query: 316 ALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKFID 375 AL +A L+ HP++EWVNYPGL + K + A+KY +G GA++ F IKGG ++FID Sbjct: 301 ALAIARHLEAHPQVEWVNYPGLPSSKYHDLAQKYLPKGA-GAVLTFGIKGGAAAGQEFID 359 Query: 376 GLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILVDL 435 +E S LANIGDAK+L IHPASTTH+Q+T +Q +AGV P +RLSVGLE +DDIL D+ Sbjct: 360 SVEFLSHLANIGDAKTLVIHPASTTHRQMTPEQQTAAGVPPDLIRLSVGLETLDDILWDI 419 Query: 436 EEAL 439 ++AL Sbjct: 420 DQAL 423 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: 556 Number of extensions: 18 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: 428 Length adjustment: 32 Effective length of query: 410 Effective length of database: 396 Effective search space: 162360 Effective search space used: 162360 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 09 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