Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_020563332.1 A3OW_RS0110145 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000372865.1:WP_020563332.1 Length = 393 Score = 509 bits (1312), Expect = e-149 Identities = 242/389 (62%), Positives = 305/389 (78%), Gaps = 1/389 (0%) Query: 13 DLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTN 72 D + +T A+RAG RT EGEH +F TSSYVF +A +A+ RF G++PGNVYSR+TN Sbjct: 5 DWNDYSLETQAIRAGHHRTHEGEHSLPIFATSSYVFNSAEEASLRFTGQLPGNVYSRFTN 64 Query: 73 PTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKY 132 PTV F+ER+A +E E+ +A ASGM+AI+A+ M L +GDHV+ SR VFG+T+ LF Y Sbjct: 65 PTVAAFQERLALMEKGERCLAFASGMAAIMAVGMGLLKAGDHVVCSRGVFGNTVLLFQNY 124 Query: 133 FKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLA 192 F +FG+ D+ L+DLAAWEAA +PNT+ F+E+PSNPL E+ D+A LA IAH G LL Sbjct: 125 FGKFGVATDFVDLTDLAAWEAAIRPNTRFLFLETPSNPLTEIADVAELASIAHRHGCLLV 184 Query: 193 VDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGG-VVAGRGEQMKEVVGFLRTAGP 251 VDNCFCTPALQ+P +LGAD+V+HSATKY+DG GR +GG V+AG K + +LRT G Sbjct: 185 VDNCFCTPALQKPFELGADIVVHSATKYLDGHGRCVGGAVIAGSEIIEKSIYPYLRTGGA 244 Query: 252 TLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARR 311 +SPFNAW+FL GLETL +RM+AH +ALALA+WLERQPG+ RVYY GLPSHPQHELARR Sbjct: 245 AMSPFNAWVFLSGLETLAVRMKAHCDNALALAQWLERQPGVSRVYYPGLPSHPQHELARR 304 Query: 312 QQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRA 371 QQS FGA+VSF++ GG++ AWR IDAT M+SIT NLGD KTTI HPATT+HGRL+PE RA Sbjct: 305 QQSHFGAIVSFELSGGKEHAWRLIDATEMLSITANLGDVKTTITHPATTTHGRLTPEVRA 364 Query: 372 RAGIGDSLIRVAVGLEDLDDLKADMARGL 400 AGI D L+RV+VGLE+++D+K D+ RGL Sbjct: 365 AAGIKDGLVRVSVGLENIEDIKKDLLRGL 393 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: 433 Number of extensions: 11 Number of successful extensions: 2 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: 393 Length adjustment: 31 Effective length of query: 372 Effective length of database: 362 Effective search space: 134664 Effective search space used: 134664 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