Align O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.- (characterized)
to candidate WP_013460790.1 SULKU_RS09695 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q9WZY4 (430 letters) >NCBI__GCF_000183725.1:WP_013460790.1 Length = 412 Score = 238 bits (607), Expect = 3e-67 Identities = 143/396 (36%), Positives = 215/396 (54%), Gaps = 11/396 (2%) Query: 31 IYQTTSYVFRDSDHAARLFALEEPGFIYTRIGNPTVSVLEERIAALEEGVGALAVASGQA 90 I + S+ + S+ +F +Y R+GNPT + LE+ +A ++ G+GA+A +SG Sbjct: 26 IVNSASFGYGSSESGEGIFEGSVKKPLYARVGNPTSAQLEQLLAQMDGGIGAVAASSGMG 85 Query: 91 AITYAILNIAGPGDEIVSGSALYGGTYNLFRHTLYKKSGIIVKFVDETDPKNIEEAITEK 150 AI A L++ GDEI+S L+GGTY+ F TL + GI F D + IEEAI Sbjct: 86 AIAMATLSLLKAGDEIISIGGLFGGTYSYFSETL-TRFGITTHFFDVDELDAIEEAINTA 144 Query: 151 TKAVYLETIGNPGLTVPDFEAIAEIAHRHGVPLIVDNTVAPYIFRPFEHGADIVVYSATK 210 TK ++LE++GNP + +PD IA IA HGV L+VDNT+ P P GADIVVYS TK Sbjct: 145 TKILFLESVGNPNMRLPDIAKIAAIAKTHGVVLMVDNTITPLSVAPITLGADIVVYSTTK 204 Query: 211 FIGGHGTSIGGLIVDSGKFDWTNGKFPELVEPDPSYHGV-SYVETFKEAAYIAKCRTQLL 269 I G+ +++GG ++ + + KF E Y + ++ A IA + + L Sbjct: 205 IITGNASALGGAVIFRA-INEGDDKFKE-----DRYRDIHPFINKMGSMALIANAKKRAL 258 Query: 270 RDLGSCMSPFNAFLFILGLETLSLRMKKHCENALKIVEFLKSHPAVSWVNYPIAEGNKTR 329 RD G + F ++L +LGLETL LRM + + + L + VN+P + Sbjct: 259 RDFGMSANGFGSYLTMLGLETLPLRMDRIVSTVEAVAKGLSARGLS--VNHPCLAHHPHH 316 Query: 330 ENALKYLKEGYGAIVTFGVKGGKEAGKKFIDSLTLISHLANIGDARTLAIHPASTTHQQL 389 E G G I+T + G KE +F++ LI+ ANIGD RTL +H AST ++ Sbjct: 317 ERYKSQFSNGCGTILTIDL-GSKERAFEFLNHSKLITITANIGDNRTLGLHMASTIYRDF 375 Query: 390 TEEEQLKTGVTPDMIRLSVGIEDVEDIIADLDQALR 425 ++ + G+TP ++R+S+G+E E II D A + Sbjct: 376 NDQTKEFLGITPGLVRISIGLESAEAIIDDFSNAAK 411 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: 431 Number of extensions: 21 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: 412 Length adjustment: 32 Effective length of query: 398 Effective length of database: 380 Effective search space: 151240 Effective search space used: 151240 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