Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_084276347.1 B8779_RS08955 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_900176045.1:WP_084276347.1 Length = 396 Score = 216 bits (551), Expect = 8e-61 Identities = 139/404 (34%), Positives = 209/404 (51%), Gaps = 27/404 (6%) Query: 25 GSRAVPIYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNPTVSVLEERIAALEEGVGALA 84 G+ + PI + ++ + D A +FA E +Y R+GNPT + LE +A +++G GA+ Sbjct: 20 GAISPPIIGSAAFSYGDPKSAEAVFAGESRKPLYARMGNPTNAKLETLLAGIDQGDGAVV 79 Query: 85 VASGQAAITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYKKSGIIVKFVDETDPKNIE 144 +SG AI + GDEIV L+GGTY F L + GI V+F + E Sbjct: 80 TSSGMGAIAAVVSAFLQSGDEIVCVGGLFGGTYAFFTQNL-PRFGIKVRFFKADE----E 134 Query: 145 EAITEKTKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVDNTVAPYIFRPFEHGADIV 204 ++ +TK ++ E++GNP LTV +F + ++A +HG+ +VDNT+ P +F PF GADI+ Sbjct: 135 VVLSPQTKMIFCESVGNPSLTVVNFVKLGKLAQKHGILFVVDNTITPLLFEPFSWGADII 194 Query: 205 VYSATKFIGGHGTSIGGLIVDSGKFDWTNGKFPELVEPDPSYHGVSYVETFKEAAYIAKC 264 VYS TK I G ++GG I+ FP L ++ E + A + Sbjct: 195 VYSTTKVISGQSQALGGAIIYKEPRKDLFIHFPFL---------QNFYENLGKDAIMGVI 245 Query: 265 RTQLLRDLGSCMSPFNAFLFILGLETLSLRMKKHCENALKIVEFLKSHPAVSWVNYPIAE 324 + + LRD G M A+L ILGLETL LR++K +NA K+ LK V + Sbjct: 246 KKRALRDFGMSMQAHAAYLTILGLETLPLRIQKATDNAQKLFLALKDKVKVLYAKNE--- 302 Query: 325 GNKTRENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLTLISHLANIGDARTLAIHPAST 384 +Y G G ++ K KE F++ + ANIGD+RTLA+H ST Sbjct: 303 ---------QYFPFGTGQMMGIDFK-SKEDAFTFLEHAKIPFITANIGDSRTLALHMRST 352 Query: 385 THQQLTEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQALRKSQ 428 ++ E GV+ ++R+SVG+E+ II D + ALRK Q Sbjct: 353 IYRDFKANELEYLGVSEGLVRISVGLENCAMIIEDFENALRKVQ 396 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: 418 Number of extensions: 25 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: 396 Length adjustment: 31 Effective length of query: 399 Effective length of database: 365 Effective search space: 145635 Effective search space used: 145635 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: 50 (23.9 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