Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012589377.1 MSIL_RS01685 O-succinylhomoserine (thiol)-lyase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000021745.1:WP_012589377.1 Length = 385 Score = 251 bits (642), Expect = 2e-71 Identities = 139/340 (40%), Positives = 207/340 (60%), Gaps = 2/340 (0%) Query: 64 GNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFG 123 G+ Y+R +NPT + +A LEG AV +SGM+AI L++ D V+ + Sbjct: 45 GHEYTRTSNPTRDLLADTLAKLEGGAGAVTLSSGMAAI-NLLLDPMERDDLVIAPHDCYS 103 Query: 124 STISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEI 183 L + + +V++ SD A A N KL +E+PSNPL +VDI A E Sbjct: 104 GVQRLLSAHAAKGHFKVEFVDQSDAEAVATALGRNPKLLMIETPSNPLMRVVDIRAFCEA 163 Query: 184 AHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQ-MKEV 242 A GA +AVDN F +PALQ+P+ LGAD V+HS TK+++G +GG V E +E+ Sbjct: 164 AKKVGAKVAVDNTFLSPALQRPIPLGADFVVHSMTKFLNGHSDVVGGAVICASESDAEEM 223 Query: 243 VGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPS 302 G+ G T SPF+++L L+GL TL R++ +A +A +L++ P +E V+Y GL S Sbjct: 224 RGWANITGVTGSPFDSYLTLRGLRTLFPRLERQQRTAETIALFLQQHPSVEAVHYPGLVS 283 Query: 303 HPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSH 362 HP H LA+ QQ+GFGA++SF+V GG A R +++ R+ ++ +LG ++ IAHPAT +H Sbjct: 284 HPSHALAKAQQAGFGAMLSFEVAGGIAAVRRLVESVRIFTLAESLGGVESLIAHPATMTH 343 Query: 363 GRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAA 402 ++PE RA AGI D+L+R++VGLE DL +D+A+ L A Sbjct: 344 ASMAPEARAAAGIKDNLLRLSVGLEHEGDLVSDLAQALKA 383 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: 350 Number of extensions: 12 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: 385 Length adjustment: 31 Effective length of query: 372 Effective length of database: 354 Effective search space: 131688 Effective search space used: 131688 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