Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_066920229.1 ACG33_RS08115 O-succinylhomoserine (thiol)-lyase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_001579945.1:WP_066920229.1 Length = 404 Score = 255 bits (652), Expect = 1e-72 Identities = 149/384 (38%), Positives = 219/384 (57%), Gaps = 15/384 (3%) Query: 21 TLAVRAGQRRTPEGEHGEA---LFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 T AVRAG + +HG L +S++ F+ GE YSR NPT Sbjct: 15 TCAVRAGLET--DDQHGAVVPPLHLSSTFAFKAF--------GERRQYDYSRSGNPTRDA 64 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFG 137 +A LEG A T+SGM+A L L + D ++ +G T L R Sbjct: 65 LATALADLEGGAGATVTSSGMAAA-QLACQLLHADDLLIAPHDCYGGTYRLLSSLAARGA 123 Query: 138 IQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCF 197 ++V + +D AA+ AA KL +VE+PSNPL +VDI A A HA GALL VDN F Sbjct: 124 LRVVFVDQTDDAAFSAALAGGPKLVWVETPSNPLLRIVDIRAAARQVHAAGALLLVDNTF 183 Query: 198 CTPALQQPLKLGADVVIHSATKYIDGQGRGMGG-VVAGRGEQMKEVVGFLRTAGPTLSPF 256 +P QQP LGAD+V+HS TKY++G +GG +V+ E + V + G T +PF Sbjct: 184 LSPVWQQPFALGADLVLHSTTKYLNGHSDVVGGALVSATAELHERVQWWANCIGVTGAPF 243 Query: 257 NAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGF 316 +++L L+G+ +L RM+AH +AL +A+ L + ++Y+ GLP+HPQH+LAR QQSGF Sbjct: 244 DSFLTLRGVRSLHARMRAHGENALQVAQLLNGHSAVRQIYFPGLPTHPQHDLARTQQSGF 303 Query: 317 GAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIG 376 GA++SF++ GG + F+D + S+ +LG ++ +AHPA+ +H + + R AGI Sbjct: 304 GAMMSFELHGGLASVRAFLDGLQCFSLAESLGGVESLVAHPASMTHAAMDAQARQAAGIS 363 Query: 377 DSLIRVAVGLEDLDDLKADMARGL 400 DSL+R+++G+E DL D+ GL Sbjct: 364 DSLLRLSIGIETAQDLLNDLQAGL 387 Lambda K H 0.319 0.133 0.392 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: 391 Number of extensions: 19 Number of successful extensions: 3 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: 403 Length of database: 404 Length adjustment: 31 Effective length of query: 372 Effective length of database: 373 Effective search space: 138756 Effective search space used: 138756 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 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