Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate 7023700 Shewana3_0930 O-acetylhomoserine/O-acetylserine sulfhydrylase (RefSeq)
Query= SwissProt::Q9WZY4 (430 letters) >FitnessBrowser__ANA3:7023700 Length = 430 Score = 456 bits (1174), Expect = e-133 Identities = 242/424 (57%), Positives = 301/424 (70%), Gaps = 10/424 (2%) Query: 12 ALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNPTVSVLEE 71 ALH GYE E T + AVPIYQTTSY F D+ H A LF L+ G IYTRI NPT SVLE+ Sbjct: 7 ALHHGYES-EATTKAAAVPIYQTTSYTFDDTQHGADLFDLKVAGNIYTRIMNPTSSVLEQ 65 Query: 72 RIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYKKSGII 131 R+AA+E G+GALA+ASG AAITYAI + GD IVS S LYGGTYNLF HTL + G+ Sbjct: 66 RLAAIEGGIGALALASGMAAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTL-PRQGVE 124 Query: 132 VKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVDNTVA- 190 V+ D + ++ I KTKA++ E+IGNP + D + +AEIAH+HGVPLIVDNTVA Sbjct: 125 VRMAAFDDFEELDALIDAKTKALFCESIGNPAGNIVDLKRLAEIAHKHGVPLIVDNTVAT 184 Query: 191 PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGK--FPELVEPDPSYHG 248 P + RPFEHGADIV++S TK+IGGHGT+IGG+I+DSGKFDW K F L + DPSYHG Sbjct: 185 PVLCRPFEHGADIVIHSLTKYIGGHGTTIGGVIIDSGKFDWVANKERFALLNQADPSYHG 244 Query: 249 VSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENALKIVEF 308 V Y E F AA+I +CR LR+ G+ +SP +AFL + GLETLSLRM++HC NAL + E+ Sbjct: 245 VVYTEAFGAAAFIGRCRVVPLRNTGAALSPHSAFLLLQGLETLSLRMERHCSNALALAEY 304 Query: 309 LKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKG-----GKEAGKKFIDSLT 363 L HP+VSWVNY + REN K I++FG+K GK AG KFID+L Sbjct: 305 LILHPSVSWVNYGALPSSPYRENCQKITGGKASGIISFGIKAATPEEGKIAGGKFIDALQ 364 Query: 364 LISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQA 423 +I L NIGDA++LA HPASTTH+QL E + GV+ D+IR+SVGIE ++DIIAD+ QA Sbjct: 365 MILRLVNIGDAKSLACHPASTTHRQLDANELARAGVSEDLIRISVGIEHIDDIIADVAQA 424 Query: 424 LRKS 427 L K+ Sbjct: 425 LEKA 428 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: 568 Number of extensions: 23 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: 430 Length adjustment: 32 Effective length of query: 398 Effective length of database: 398 Effective search space: 158404 Effective search space used: 158404 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