Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_092997718.1 BLP65_RS12545 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_900102855.1:WP_092997718.1 Length = 395 Score = 531 bits (1367), Expect = e-155 Identities = 254/389 (65%), Positives = 311/389 (79%) Query: 12 SDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYT 71 +D + F+T AVRAGQ RT EGE EA+F TSS+ F TAA AAARF+G+ GN+YSR+T Sbjct: 2 TDWDEYGFETRAVRAGQVRTLEGEQSEAIFATSSFTFDTAAQAAARFSGQESGNIYSRFT 61 Query: 72 NPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDK 131 NPTVRTFEER+AALEG E+ VAT SGMSAIL+ M L SGDH++ S ++FGST+SLF+ Sbjct: 62 NPTVRTFEERLAALEGGERCVATGSGMSAILSTCMGLLKSGDHIVASTALFGSTVSLFEN 121 Query: 132 YFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALL 191 Y K+FGI + Y PL+DL AW+ A +P T+L F+E+PSNPL E+ D+ ALA +AHA L Sbjct: 122 YLKKFGIGISYVPLTDLTAWQEAIRPETRLLFLETPSNPLTEVADVEALAALAHASECRL 181 Query: 192 AVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGP 251 VDNCFCTPALQ+PL++GAD+VIHSATKYIDGQGR +GG V G E M+ V GFLRTAGP Sbjct: 182 VVDNCFCTPALQRPLEMGADIVIHSATKYIDGQGRCIGGAVVGSDELMEPVFGFLRTAGP 241 Query: 252 TLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARR 311 T+SPFNAW+FLKGLETL +RM+AHS +AL LA WL +QP + RV+Y GL HPQH LA R Sbjct: 242 TMSPFNAWVFLKGLETLSLRMKAHSENALLLARWLAKQPAVARVHYPGLVDHPQHALAAR 301 Query: 312 QQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRA 371 QQ FG +V+F+V GGR+AAWR ID+TRM+SIT NLGDTKTTI HPATT+HGRLS E R Sbjct: 302 QQKAFGGIVAFEVAGGREAAWRIIDSTRMLSITANLGDTKTTITHPATTTHGRLSAEQRE 361 Query: 372 RAGIGDSLIRVAVGLEDLDDLKADMARGL 400 AGI + LIR++VGLED+ D++AD+ARGL Sbjct: 362 SAGINEDLIRISVGLEDVTDIQADLARGL 390 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: 469 Number of extensions: 10 Number of successful extensions: 1 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: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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