Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_092348401.1 BLU87_RS11360 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_900107645.1:WP_092348401.1 Length = 427 Score = 542 bits (1396), Expect = e-159 Identities = 268/424 (63%), Positives = 325/424 (76%), Gaps = 3/424 (0%) Query: 5 KYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNP 64 KY T ALHAG + P+ T SRAVPIYQT+SY F ++HAA LF+L+E G IYTR+ NP Sbjct: 6 KYQDGTLALHAG-QVPDPTTNSRAVPIYQTSSYTFDSAEHAANLFSLKEMGNIYTRLMNP 64 Query: 65 TVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTL 124 T VLE+R+A L+ GVGALA+ASG AA+T AI+NIA GD I++ S LYGGT+NLF HT Sbjct: 65 TTDVLEKRLAELDGGVGALALASGSAAVTLAIMNIAQCGDNIITSSCLYGGTFNLFHHT- 123 Query: 125 YKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLI 184 +K+ GI VKFVD ++P N+ AI + TKA+Y ETIGNP V DFEA+A++AH +G+P I Sbjct: 124 FKRMGIGVKFVDTSNPANVAAAIDDNTKALYTETIGNPKNNVDDFEALAKVAHDNGIPFI 183 Query: 185 VDNTVA-PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELVEPD 243 VDNTVA P +F+P EHGADIV YS TKFIGGHGTSIGG +VDSG FDWT+G+F E PD Sbjct: 184 VDNTVATPLLFKPIEHGADIVCYSLTKFIGGHGTSIGGAVVDSGNFDWTSGRFTEFTTPD 243 Query: 244 PSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENAL 303 PSYHG+ Y E AYI K R LLRD+G C+SP NAF F+ GLETL +RM +HCENAL Sbjct: 244 PSYHGLVYHEALGNLAYILKMRLTLLRDMGPCLSPTNAFNFLQGLETLHVRMPRHCENAL 303 Query: 304 KIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLT 363 K+ +FL+ HP V+W+NYP E +K +N +YL +G GAI+ FG+KGG E+ KFID + Sbjct: 304 KVAQFLEQHPQVTWINYPGLESHKDYQNGQRYLPKGQGAIIGFGIKGGAESSAKFIDKVK 363 Query: 364 LISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQA 423 L SHLANIGDA+TL +HPASTTHQQL EEQL GVTPD IR+SVGIED+EDIIADLDQA Sbjct: 364 LASHLANIGDAKTLVVHPASTTHQQLNAEEQLTAGVTPDYIRISVGIEDIEDIIADLDQA 423 Query: 424 LRKS 427 L S Sbjct: 424 LNAS 427 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: 578 Number of extensions: 20 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: 430 Length of database: 427 Length adjustment: 32 Effective length of query: 398 Effective length of database: 395 Effective search space: 157210 Effective search space used: 157210 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