Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate Synpcc7942_0370 Synpcc7942_0370 O-acetylhomoserine/O-acetylserine sulfhydrylase
Query= BRENDA::P94890 (442 letters) >FitnessBrowser__SynE:Synpcc7942_0370 Length = 434 Score = 501 bits (1290), Expect = e-146 Identities = 243/425 (57%), Positives = 315/425 (74%), Gaps = 1/425 (0%) Query: 16 ETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTTDVL 75 ET+ALH GQ+PDPTT SRAVP+YQTTSYVF+D +HAA LF L+ FGNIYTRLMNPTTDVL Sbjct: 6 ETLALHAGQKPDPTTGSRAVPIYQTTSYVFEDAEHAANLFALKAFGNIYTRLMNPTTDVL 65 Query: 76 EKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPKLGI 135 E+R+AAL GG A+AT+SGQ+A A+ I AGQ I+++++LYGGT NL +T + GI Sbjct: 66 EQRLAALHGGTGAVATSSGQAAIFYAIAAITSAGQNIISTTNLYGGTINLFRHTLKRFGI 125 Query: 136 KVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDNTMP 195 +V FVD SD + A ++ TR Y E++GNPK + D A++ +A + G+P ++DNT+ Sbjct: 126 EVRFVDSSDASSVAAAIDENTRLVYTESIGNPKGNVDDFEAIAAIAHDSGIPFIVDNTVS 185 Query: 196 SPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGKFKNFTEPDPSYHGL 255 P L NPL+HGAD+VV SLTK GGHGTS+GGI+I+ G F W NGKF PDPSYHG+ Sbjct: 186 PPPLFNPLEHGADVVVLSLTKLAGGHGTSLGGIVIEKGDFPWNNGKFPEIAGPDPSYHGV 245 Query: 256 KFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERHSGN 315 FW+ FG +A++LK R LRD+G +SPFNA Q+L GVETLPLR ERH N Sbjct: 246 NFWDAFGNHPEAVAPGLAYVLKIRTGLLRDIGATLSPFNAQQVLLGVETLPLRAERHVRN 305 Query: 316 ALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKKFID 375 A VAE+L++HP + WVNYPGL + +Y A++Y G GAI+GF ++GG+E K+FI Sbjct: 306 AQAVAEWLERHPLVTWVNYPGLPSHPDYDRAQRYLPNGA-GAILGFGVQGGLEAGKRFIS 364 Query: 376 GLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDILVDL 435 ++L S LAN+ DAK+L IHPASTTHQQL+ EQ +AGV+P FVRLSVGLE++DDIL DL Sbjct: 365 AVKLASNLANVLDAKTLVIHPASTTHQQLSPEEQAAAGVSPDFVRLSVGLEHLDDILADL 424 Query: 436 EEALK 440 ++AL+ Sbjct: 425 DQALQ 429 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: 568 Number of extensions: 18 Number of successful extensions: 2 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: 434 Length adjustment: 32 Effective length of query: 410 Effective length of database: 402 Effective search space: 164820 Effective search space used: 164820 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