Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate AZOBR_RS07765 AZOBR_RS07765 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::Q9WZY4 (430 letters) >FitnessBrowser__azobra:AZOBR_RS07765 Length = 429 Score = 454 bits (1169), Expect = e-132 Identities = 230/423 (54%), Positives = 303/423 (71%), Gaps = 3/423 (0%) Query: 4 KKYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGN 63 K +G+ TRA+HAG P+ ATG+R PIYQTTS+VF D D AA LF L++ GFIY+R+ N Sbjct: 5 KSFGFETRAIHAG-AAPDPATGARQTPIYQTTSFVFDDVDDAASLFNLQKVGFIYSRLTN 63 Query: 64 PTVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHT 123 PTVSVLEER+A LE G GA A +SG AA A+ + PGDEIV+ LYGGT N + Sbjct: 64 PTVSVLEERLANLEGGAGATATSSGHAAQLLALFPLMEPGDEIVASRKLYGGTLNQLGTS 123 Query: 124 LYKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPL 183 + G FVD P+N+ AIT KTKA+++E++ NPG V D EAIA+IA G+PL Sbjct: 124 FPRAFGWKSVFVDTDQPENVRAAITAKTKAIFVESLANPGGVVTDLEAIAKIADEAGIPL 183 Query: 184 IVDNTVA-PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDW-TNGKFPELVE 241 IVDNT+A PY+ P + GA +VV+S TKF+ G+GTS+GG+++DSG FDW +GKFP L E Sbjct: 184 IVDNTLATPYLINPIQWGATLVVHSTTKFLSGNGTSVGGVVIDSGSFDWGKSGKFPALSE 243 Query: 242 PDPSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCEN 301 PD YHG+ + ETF A+ LRDLG +P NAFL + G+ETL LRM++H ++ Sbjct: 244 PDAGYHGLKFQETFGHLAFTIHGHAVGLRDLGPSQAPLNAFLTLNGIETLPLRMQRHSDS 303 Query: 302 ALKIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDS 361 ALK+ +FL+SHPAV WV+Y E +K A KYL +G GA++TFGVKGG + G K +++ Sbjct: 304 ALKVAQFLESHPAVGWVSYAGLESSKYNALAKKYLPKGAGAVLTFGVKGGFDTGVKVVEN 363 Query: 362 LTLISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLD 421 + L+SHLANIGD+R+L IHP+STTH+QL+ E Q + G PD++RLS+G+E VEDIIADLD Sbjct: 364 VQLLSHLANIGDSRSLIIHPSSTTHRQLSPEGQAQAGAGPDVLRLSIGLESVEDIIADLD 423 Query: 422 QAL 424 +AL Sbjct: 424 RAL 426 Lambda K H 0.317 0.136 0.398 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: 561 Number of extensions: 23 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: 430 Length of database: 429 Length adjustment: 32 Effective length of query: 398 Effective length of database: 397 Effective search space: 158006 Effective search space used: 158006 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