Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_074201059.1 BUQ81_RS03740 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_900141795.1:WP_074201059.1 Length = 391 Score = 502 bits (1292), Expect = e-147 Identities = 238/382 (62%), Positives = 300/382 (78%), Gaps = 1/382 (0%) Query: 20 DTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79 +T A+ G RRTPEGE+ EA+F TSS+ F +AA AAARF+G+ PGN+YSR+TNPTVRTFE Sbjct: 6 ETFAIHGGYRRTPEGENSEAIFPTSSFAFDSAAQAAARFSGDEPGNIYSRFTNPTVRTFE 65 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139 +R+AA+EG E V TASGMSAIL+L++ + SGDH++ S+S+FG+T LF KY + GI Sbjct: 66 QRLAAMEGGEACVGTASGMSAILSLMLGMLESGDHIVSSQSIFGTTKVLFSKYLGKLGID 125 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 Y PL+D AW AA +P T++ F+E+PSNP+ ++ DI LAEIAHA LL VDNCFCT Sbjct: 126 TTYVPLTDYDAWAAAIRPETRMLFLETPSNPMTDVADIQRLAEIAHAHDCLLVVDNCFCT 185 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKE-VVGFLRTAGPTLSPFNA 258 PALQQPLKLGAD+VIHSATK++DGQGR +GG V G ++E V GFLRT GP++SPFNA Sbjct: 186 PALQQPLKLGADLVIHSATKFLDGQGRCVGGAVVGPESLVEEHVRGFLRTCGPSMSPFNA 245 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318 W+F KGLETL +RMQAHSA+ALALA+WL P +E+V+Y GLPSHPQHELA RQQ G Sbjct: 246 WVFFKGLETLHVRMQAHSANALALAQWLSDHPAVEQVFYPGLPSHPQHELAMRQQKAGGG 305 Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378 +VSF +KGGR AW+ +D+ M+ IT NLGDTKT I HPATT+H R+ PE R AGI D+ Sbjct: 306 LVSFRIKGGRGDAWKVVDSLEMIHITANLGDTKTLITHPATTTHSRVEPEARLAAGITDN 365 Query: 379 LIRVAVGLEDLDDLKADMARGL 400 L+RV+VGLE ++D+KAD+ RGL Sbjct: 366 LLRVSVGLESIEDIKADLGRGL 387 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: 447 Number of extensions: 10 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: 391 Length adjustment: 31 Effective length of query: 372 Effective length of database: 360 Effective search space: 133920 Effective search space used: 133920 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