Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_026606931.1 METAC_RS0110085 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000427445.1:WP_026606931.1 Length = 425 Score = 298 bits (762), Expect = 3e-85 Identities = 171/420 (40%), Positives = 240/420 (57%), Gaps = 8/420 (1%) Query: 8 YNTRALHAGYEPPEQATGSRAVPIYQTT-SYVFRDSDHAARLFALEEPGFIYTRIGNPTV 66 + T+ALHAG E G P + S VF +A+ + + + V Sbjct: 9 FATKALHAGAERDHSLCGG--APAHSDIWSMVFDSDANASPSLRPSRLCGVQMQAESRAV 66 Query: 67 SVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYK 126 ++LEERIAALEEGV A+A ASG+ A+ + PG++I++ A GG + H + Sbjct: 67 ALLEERIAALEEGVAAVAFASGRGALLATFHLLMKPGEDIIAARAARGGAMDQLAHG-FG 125 Query: 127 KSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVD 186 G+ +K+ D D AI +TKA+++E+ PG + D EAI +A G+PLIVD Sbjct: 126 DFGMRIKWADPMDLSTFTAAIGPRTKAIFVESTWGPGGAIVDLEAIGSVAKSVGIPLIVD 185 Query: 187 NTVA-PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNG-KFPELVEPDP 244 NT A PY+ RPFEHGADIVV+SA + G G GGLI+D G F+W ++P L P P Sbjct: 186 NTAATPYLVRPFEHGADIVVHSAAALLSGRGDQRGGLIIDGGGFNWLQDERYPMLSAPRP 245 Query: 245 SYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENALK 304 + G TF ++ R L G ++P +A L + G+ETL+LRM++HCENA Sbjct: 246 EFDGTILANTFGNFSFAVAARALGLGHFGCELAPLDALLILAGVETLALRMQRHCENART 305 Query: 305 IVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLTL 364 I E L HPAV WV+YP G+++ A KY G GA +T G+ GG A + L L Sbjct: 306 IAEHLARHPAVRWVSYPGLSGDRSNALAQKYCPNGAGAALTLGLTGGYPAAAAVVSRLKL 365 Query: 365 ISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQAL 424 S L+N GDAR+ A+HPAS+ ++ + + + + PD++RLS+GIED DIIADLDQAL Sbjct: 366 FSALSNFGDARSRALHPASSAERRPSYDGE--SDEPPDLVRLSIGIEDTNDIIADLDQAL 423 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: 483 Number of extensions: 21 Number of successful extensions: 5 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: 425 Length adjustment: 32 Effective length of query: 398 Effective length of database: 393 Effective search space: 156414 Effective search space used: 156414 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