Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_012566511.1 RC1_RS06305 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000016185.1:WP_012566511.1 Length = 437 Score = 457 bits (1175), Expect = e-133 Identities = 233/425 (54%), Positives = 297/425 (69%), Gaps = 3/425 (0%) Query: 2 DWKKYGYNTRALHAGYEPPEQATGSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRI 61 D + G+ TRA+HAG P+ TG+RA PIYQTTSYVF D + AA LF LE+ GFIY+R+ Sbjct: 3 DSRSSGFETRAIHAG-AAPDPTTGARATPIYQTTSYVFDDVEDAAALFNLEKVGFIYSRL 61 Query: 62 GNPTVSVLEERIAALEEGVGALAVASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFR 121 NPTVSVLE R+A LE G GA +SG AA A+ + PGDEIV+ LYGGT N F Sbjct: 62 TNPTVSVLEARLADLEGGAGATCTSSGHAAQLLALFPLLTPGDEIVASRQLYGGTLNQFA 121 Query: 122 HTLYKKSGIIVKFVDETDPKNIEEAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGV 181 ++ + G FVD DP+N A+T KTKA+++E++ NPG V D EAIA IA G+ Sbjct: 122 NSFPRAFGWKTVFVDSDDPENFRRALTPKTKAIFIESLANPGGVVLDIEAIARIADGAGI 181 Query: 182 PLIVDNTVA-PYIFRPFEHGADIVVYSATKFIGGHGTSIGGLIVDSGKFDWT-NGKFPEL 239 PLIVDNT+A PY+ RP +HGA +VV+S TKF+GGHG S+GG+++DSG+FDW+ +G+FP L Sbjct: 182 PLIVDNTLATPYLCRPLDHGATLVVHSTTKFLGGHGNSVGGVVIDSGRFDWSKDGRFPAL 241 Query: 240 VEPDPSYHGVSYVETFKEAAYIAKCRTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHC 299 EP+P YHG+ + TF A+ LRDLG +P NAFL + G+ETL+LRM++H Sbjct: 242 SEPEPGYHGMRFHATFGALAFTIHGHAIGLRDLGPSQAPLNAFLTLTGIETLALRMERHS 301 Query: 300 ENALKIVEFLKSHPAVSWVNYPIAEGNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFI 359 NAL + + LK HPAV+WVNY ++ A KYL G G++ TFG+KGG EAG K + Sbjct: 302 ANALAVAQHLKQHPAVAWVNYAGLPDSRYHALARKYLPRGAGSVFTFGLKGGYEAGVKLV 361 Query: 360 DSLTLISHLANIGDARTLAIHPASTTHQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIAD 419 +S+ L SHLANIGD R+L IHPASTTH QL+ E G PD++RLSVGIE VEDIIAD Sbjct: 362 ESVKLFSHLANIGDTRSLIIHPASTTHSQLSPEGLAAAGAGPDVVRLSVGIESVEDIIAD 421 Query: 420 LDQAL 424 LDQAL Sbjct: 422 LDQAL 426 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: 579 Number of extensions: 28 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: 437 Length adjustment: 32 Effective length of query: 398 Effective length of database: 405 Effective search space: 161190 Effective search space used: 161190 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