Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_028989181.1 G579_RS0104235 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000423825.1:WP_028989181.1 Length = 397 Score = 508 bits (1308), Expect = e-148 Identities = 249/393 (63%), Positives = 307/393 (78%), Gaps = 1/393 (0%) Query: 11 DSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRY 70 D++ E DTLAVRAG TPEGEH E +F TSSYVF++AA+AAARFAG+ PGNVYSRY Sbjct: 4 DNNWEDWQPDTLAVRAGVHTTPEGEHSEPIFPTSSYVFQSAAEAAARFAGQ-PGNVYSRY 62 Query: 71 TNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFD 130 TNPTVR FEER+AALEGAE VAT SGM+A LA M+L +GDHV+ SR++FG+T+ L Sbjct: 63 TNPTVRAFEERLAALEGAESCVATGSGMAACLATFMALLKAGDHVVASRAIFGTTVQLLS 122 Query: 131 KYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGAL 190 RFG++ + L+DL AW AA +PNT++ F+E+PSNP+ E+ D+AALA IAH GA Sbjct: 123 NILGRFGLETTFVDLTDLGAWRAAIRPNTRMLFLETPSNPMTEIGDLAALAAIAHEAGAR 182 Query: 191 LAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAG 250 L VDN FCTP LQ+PL GADVVI SATKYIDG GR +GG V G E M+ GFLRTAG Sbjct: 183 LVVDNTFCTPVLQRPLDFGADVVIQSATKYIDGHGRCLGGAVLGSRELMEGPRGFLRTAG 242 Query: 251 PTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELAR 310 P++SPFNAW+FLKGLETL +RM H+ASA ALAEWLE QP + RV+Y GL SHPQH LA+ Sbjct: 243 PSMSPFNAWVFLKGLETLSLRMARHNASAQALAEWLEAQPQVNRVFYPGLASHPQHALAQ 302 Query: 311 RQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDR 370 RQQ G G ++SFD+KGG+ AAW F+DA R+ S+T NLGD KTT+ H A+T+H R+SPE R Sbjct: 303 RQQKGPGGILSFDLKGGQPAAWAFLDALRICSLTANLGDAKTTVTHAASTTHSRVSPEAR 362 Query: 371 ARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 A AGI D L+R++VGLED++DL+ D+ARGLAA+ Sbjct: 363 AAAGITDGLVRISVGLEDVEDLRQDLARGLAAI 395 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: 473 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: 397 Length adjustment: 31 Effective length of query: 372 Effective length of database: 366 Effective search space: 136152 Effective search space used: 136152 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