Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_014147972.1 MEALZ_RS07275 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000968535.2:WP_014147972.1 Length = 396 Score = 499 bits (1286), Expect = e-146 Identities = 233/388 (60%), Positives = 304/388 (78%), Gaps = 1/388 (0%) Query: 11 DSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRY 70 D+D + +T A+RAG RRT E EH +F TSSYVF +A +A+ +F G++PGN+YSR+ Sbjct: 3 DTDWNDYSLETQAIRAGHRRTGEAEHSIPIFMTSSYVFDSAEEASLKFTGQIPGNIYSRF 62 Query: 71 TNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFD 130 TNPTV F+ER+A +E E+ +A ASGM+AI+A+ M L SGDHV+VSR VFG+T+ +F Sbjct: 63 TNPTVNAFQERLAWMENGERCLAFASGMAAIMAVGMGLLKSGDHVVVSRGVFGNTVLMFQ 122 Query: 131 KYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGAL 190 YF +FG++ D+ L+DLAAWEAA KPNT+ F+E+PSNPL E+ DI ALA++AH L Sbjct: 123 NYFAKFGVESDFVALTDLAAWEAAIKPNTRFLFLETPSNPLTEIADIQALADLAHRHDCL 182 Query: 191 LAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQM-KEVVGFLRTA 249 L VDNCFCTPALQ+PL LGAD+++HSATKYIDG GR +GG V E + K + +LRT Sbjct: 183 LIVDNCFCTPALQKPLDLGADIIVHSATKYIDGHGRCVGGAVVASDEIIEKAIYPYLRTG 242 Query: 250 GPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELA 309 G T+SPFNAW FL GLETL +RM+ H A+AL LA WLERQPG+ERV+Y GL SHPQHELA Sbjct: 243 GATMSPFNAWAFLSGLETLALRMEKHCANALDLARWLERQPGVERVHYPGLVSHPQHELA 302 Query: 310 RRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPED 369 +RQQ+GFG +VSF++KGG++ AW ID+TRM+SIT NLGD K+TI HPATT+HGRL+PE Sbjct: 303 KRQQTGFGGIVSFELKGGKEPAWNLIDSTRMISITANLGDVKSTITHPATTTHGRLTPEA 362 Query: 370 RARAGIGDSLIRVAVGLEDLDDLKADMA 397 R AGI D L+R++VGLE+++D+K D++ Sbjct: 363 RDAAGIKDGLVRISVGLENIEDIKKDLS 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: 439 Number of extensions: 13 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: 396 Length adjustment: 31 Effective length of query: 372 Effective length of database: 365 Effective search space: 135780 Effective search space used: 135780 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