Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_046009022.1 OLEAN_RS09365 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000967895.1:WP_046009022.1 Length = 405 Score = 522 bits (1345), Expect = e-153 Identities = 251/395 (63%), Positives = 317/395 (80%) Query: 9 RLDSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYS 68 R SDL A F+TLAVRAG R+ GEH EA++ TSSYVF +AA+AAARF+G+ GNVYS Sbjct: 10 RYQSDLTDADFETLAVRAGHVRSANGEHSEAIYLTSSYVFNSAAEAAARFSGDEEGNVYS 69 Query: 69 RYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISL 128 RYTNPTVRTFEER+AALEG E ATASGM+AI ++V++ +GD ++VSR+VFGST L Sbjct: 70 RYTNPTVRTFEERLAALEGGEDCAATASGMAAIYSVVIAHLKAGDSIVVSRNVFGSTNVL 129 Query: 129 FDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKG 188 F+K+ ++F I V Y L DL AW A T++ F+ESPSNP++E+ D+ ALA++AH Sbjct: 130 FEKFVRKFNIDVRYVDLLDLKAWAEAIDSTTRMLFLESPSNPMSEIADLQALADLAHKHD 189 Query: 189 ALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRT 248 ALL VDNCFCTPALQQPLK GAD++IHSATKYIDGQGR +GG V G + ++ V+G LR+ Sbjct: 190 ALLVVDNCFCTPALQQPLKFGADLIIHSATKYIDGQGRCLGGAVVGSKQLIEPVIGVLRS 249 Query: 249 AGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHEL 308 AGPTLSPFNAW+FLKGLETL +RM+AHS +A+ LA WL++Q I +V Y+GL HP HEL Sbjct: 250 AGPTLSPFNAWVFLKGLETLSLRMKAHSENAMVLARWLQQQSQITKVNYSGLEDHPGHEL 309 Query: 309 ARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPE 368 A++QQS FG V+SF+VKGG+ AAW+ ID TRM+SIT NLGDTKTT+ HPA+T+H RLSPE Sbjct: 310 AKKQQSAFGGVLSFEVKGGQQAAWQLIDGTRMISITANLGDTKTTVTHPASTTHSRLSPE 369 Query: 369 DRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 DRARAGIGD L+R+AVGLE ++D++ D+A GLAA+ Sbjct: 370 DRARAGIGDGLVRIAVGLESIEDIQKDIALGLAAI 404 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: 458 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: 405 Length adjustment: 31 Effective length of query: 372 Effective length of database: 374 Effective search space: 139128 Effective search space used: 139128 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