Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_041245581.1 GURA_RS20075 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase family protein
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000016745.1:WP_041245581.1 Length = 417 Score = 350 bits (898), Expect = e-101 Identities = 189/421 (44%), Positives = 267/421 (63%), Gaps = 14/421 (3%) Query: 5 KYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNP 64 KY ++T +H G EP G+ VPI Q++S+ ++ +F + G +YTR+GNP Sbjct: 7 KYSFDTLLIHGGLEPGP--AGATTVPIVQSSSFAQATAEELEDIFRGRKVGQVYTRVGNP 64 Query: 65 TVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTL 124 T LE+R+A LE G A+A ASG AAIT A++ I GDEI++ S+L+GGT++LFR TL Sbjct: 65 TTESLEKRLALLEGGQAAIATASGMAAITTAVMTIVRSGDEILASSSLFGGTFSLFRDTL 124 Query: 125 YKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLI 184 GI FVD TD + I ++T+ V++ETIGNP + VPD AIA IA G+PL+ Sbjct: 125 -SGYGISTTFVDPTDLAAVRNGINDRTRLVFVETIGNPKMDVPDIPAIALIARAAGIPLL 183 Query: 185 VDNTV-APYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELVEPD 243 VD TV P + R + GADIV++S +KFI G G++IGG+I+D G+FDW + KFP Sbjct: 184 VDATVTTPCLARGSDLGADIVIHSTSKFINGTGSAIGGVIIDLGRFDWQSDKFP------ 237 Query: 244 PSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENAL 303 H + + ++ A+ A+ R + +D G+C +P N+FL G+ETLSLRM++HC NA Sbjct: 238 ---HFEPFHKKYRAFAFTARARKLIHKDFGACAAPMNSFLLAEGVETLSLRMERHCANAQ 294 Query: 304 KIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLT 363 K+ +FLK+H V WVNYP E + + A K + +G ++TFG+ K A +FI+ + Sbjct: 295 KLAQFLKAHDRVRWVNYPGLEDSPHHQVAKKLYGDKFGGVLTFGL-ADKAAAFRFINGVR 353 Query: 364 LISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQA 423 L +LANIGDA+TL IHPAST EE+ GV +M+R+SVGIE + DII D D A Sbjct: 354 LAKNLANIGDAKTLVIHPASTICCDYGPEEKGLMGVGEEMVRVSVGIEAINDIIEDFDSA 413 Query: 424 L 424 L Sbjct: 414 L 414 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: 457 Number of extensions: 21 Number of successful extensions: 6 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: 417 Length adjustment: 32 Effective length of query: 398 Effective length of database: 385 Effective search space: 153230 Effective search space used: 153230 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 12 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