Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Ac3H11_2928 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= SwissProt::P9WGB5 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2928 Length = 436 Score = 233 bits (595), Expect = 6e-66 Identities = 137/405 (33%), Positives = 216/405 (53%), Gaps = 40/405 (9%) Query: 37 AEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSRYGNPTVSVFEERLRLIEGAPAAFATAS 96 A ++LT+ +V+ S+ A F E +VYSR NPT +V E+R+ +EG A ATAS Sbjct: 28 ATPIHLTTSFVFESSDHAASLFNLERGGHVYSRISNPTNAVLEQRVAALEGGVGAIATAS 87 Query: 97 GMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTVFVDGDDLSQWERALS 156 G AA+ ++ ++GAG +VA+ +L+G + L R+G++T FV D+ W A+ Sbjct: 88 GQAALHLAIATIMGAGSHIVASTALYGGSQNLLHYTLSRFGIETTFVKPGDIDAWRAAVR 147 Query: 157 VPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFATPLLQQGFPLGVDVVVYS 216 T+ F ET NP ++DI V+ +AH AG +++D+ +P L + F G D+V +S Sbjct: 148 PNTKLFFGETVGNPGLDVLDIPTVSSIAHEAGVPLLVDSTLTSPWLIKPFEHGADLVYHS 207 Query: 217 GTKHIDGQGRVLGGAILGDREY-IDGPV-------------------------------- 243 TK + G G V+GG ++ + DGP Sbjct: 208 ATKFLSGHGTVVGGIVVDGGSFDWDGPKSAGKFAELTQPYDGFHNMVFTEESTVGAFLLR 267 Query: 244 --QKLMRHTGPAMSAFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYL 301 ++ +R G MS AW++L+G+ETL +R+ + +++ EFL P V V +P L Sbjct: 268 ARREGLRDFGACMSPHTAWLILQGIETLPLRMAQHMRNTEKVVEFLAAQPFVSRVGHPML 327 Query: 302 PSHPQYDLAKRQM-SGGGTVVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVT 360 SHP + LA++ + G G+V +F L + K + ++ +++ N+GD +SLV Sbjct: 328 ESHPSHALAQKLLPRGAGSVFSFDLKGNREQGK----KFIETLKVFSHLANVGDCRSLVI 383 Query: 361 HPATTTHRAMGPEGRAAIGLGDGVVRISVGLEDTDDLIADIDRAL 405 HPA+TTH M E A G+ G +R+S+GLED DDLI D+ RAL Sbjct: 384 HPASTTHFRMSDEALAGAGITQGTIRLSIGLEDADDLIDDLKRAL 428 Lambda K H 0.319 0.135 0.395 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: 467 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 406 Length of database: 436 Length adjustment: 32 Effective length of query: 374 Effective length of database: 404 Effective search space: 151096 Effective search space used: 151096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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