Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_092056756.1 BQ4888_RS09550 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_900111775.1:WP_092056756.1 Length = 429 Score = 541 bits (1394), Expect = e-158 Identities = 272/428 (63%), Positives = 328/428 (76%), Gaps = 3/428 (0%) Query: 2 DWKKYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRI 61 D+ G TRALHAG + P+ ATGSRAVPIYQT+SYVF ++HAA LFAL+E G IYTR+ Sbjct: 3 DFHPQGIGTRALHAG-QVPDPATGSRAVPIYQTSSYVFNSTEHAANLFALKEMGNIYTRL 61 Query: 62 GNPTVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFR 121 NPT VLE+R+AAL+ GVGALA++SG +AI AILN+A GD IVS S+LYGGT+NLFR Sbjct: 62 MNPTTDVLEKRLAALDGGVGALALSSGSSAIFLAILNLARTGDNIVSSSSLYGGTHNLFR 121 Query: 122 HTLYKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGV 181 HTL + GI VKFVD + ++I AI TKAV+ E+IGNP V DF AIA+IAH+HG+ Sbjct: 122 HTL-GRMGIAVKFVDTSRLESITAAIDGNTKAVFTESIGNPKNNVDDFAAIAKIAHKHGL 180 Query: 182 PLIVDNTVAPY-IFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELV 240 P IVDNTVA +FRP EHGADIV YS TKFIGGHGTS+GG ++DSG FDW +G+FPE Sbjct: 181 PFIVDNTVATAALFRPIEHGADIVCYSLTKFIGGHGTSVGGAVIDSGNFDWASGRFPEFT 240 Query: 241 EPDPSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCE 300 PDPSYHG+ Y + + AYI K R LLRDLG C+SPFNAF F+ GLETL +RM +HC+ Sbjct: 241 SPDPSYHGLIYHQALGQLAYILKMRLTLLRDLGPCLSPFNAFQFLQGLETLHVRMPRHCD 300 Query: 301 NALKIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFID 360 NAL + FL+ HPAV+WVNYP E + NAL+YL +G GAI+ FG+KGG +FID Sbjct: 301 NALALAHFLEGHPAVAWVNYPGLENHPDHANALRYLPKGQGAIIGFGIKGGAAGAARFID 360 Query: 361 SLTLISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADL 420 + L SHLANIGDA+TL IHPASTTHQQLT EEQ GV+ D IR+SVGIED++DI+ADL Sbjct: 361 GVKLASHLANIGDAKTLVIHPASTTHQQLTPEEQRSAGVSEDFIRVSVGIEDIDDILADL 420 Query: 421 DQALRKSQ 428 DQALR SQ Sbjct: 421 DQALRASQ 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: 574 Number of extensions: 24 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 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