Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012536942.1 AFE_RS09520 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000021485.1:WP_012536942.1 Length = 404 Score = 491 bits (1263), Expect = e-143 Identities = 236/385 (61%), Positives = 297/385 (77%), Gaps = 1/385 (0%) Query: 20 DTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79 +T+A+RAG RT E EH EA+F TSS+VF +A +AA RFAG VPGN+Y+R+TNPTVRTFE Sbjct: 17 ETIAIRAGIHRTQEQEHSEAIFPTSSFVFDSAEEAADRFAGRVPGNIYARFTNPTVRTFE 76 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139 ER+AALEGAE VATASGM+A L M + +GDHV+ SRS+FG+T+ L RFG++ Sbjct: 77 ERLAALEGAEACVATASGMAACLTAFMGILKAGDHVVASRSIFGTTVQLLGNILSRFGVE 136 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 + PL+D+ AW AA +PNT++ F+E+PSNPL E+ D+ ALA++AH A L VDNCFCT Sbjct: 137 TSFVPLADVPAWRAALRPNTRMLFLETPSNPLTEIGDMQALADLAHVHDAWLVVDNCFCT 196 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKE-VVGFLRTAGPTLSPFNA 258 PALQQPLK GAD+VIHSATKY+DGQGR +GG V G E + F+RTAGP+LSPFNA Sbjct: 197 PALQQPLKFGADLVIHSATKYLDGQGRTLGGAVCGSTELLNSGPRNFVRTAGPSLSPFNA 256 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318 W+ LKGLETL +RM+ H A+A +AEWLE +P + RVYY GL SHPQ LA RQQ GA Sbjct: 257 WVQLKGLETLGLRMERHCANAQKIAEWLEARPEVARVYYPGLDSHPQQALAARQQRLPGA 316 Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378 ++SFD+ GG+ AAW F+DA R++S+T NLGD KTTI HPA+T+H R+SPE RA AG+GD Sbjct: 317 ILSFDLHGGQKAAWAFVDALRLLSLTANLGDAKTTITHPASTTHSRVSPEARAAAGVGDG 376 Query: 379 LIRVAVGLEDLDDLKADMARGLAAL 403 L+R++VGLE DDL+ DM RG AAL Sbjct: 377 LLRISVGLEHADDLREDMERGFAAL 401 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: 488 Number of extensions: 17 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: 404 Length adjustment: 31 Effective length of query: 372 Effective length of database: 373 Effective search space: 138756 Effective search space used: 138756 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