Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_011800504.1 PNAP_RS05450 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000015505.1:WP_011800504.1 Length = 404 Score = 459 bits (1181), Expect = e-134 Identities = 235/391 (60%), Positives = 293/391 (74%), Gaps = 7/391 (1%) Query: 20 DTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFE 79 DTLAVR G R+ GE+ EAL+ TS +V A +A RFAG G Y+R +NPTV FE Sbjct: 13 DTLAVRVGIERSQYGENSEALYLTSGFVQPDAETSARRFAGTEEGFTYARTSNPTVAAFE 72 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139 +R+AALEG E A+A +SGM AIL + M L +GDHV+ S+SVFGST++LF K F +FG++ Sbjct: 73 QRLAALEGTEAAIAASSGMGAILMMGMGLLRAGDHVVCSQSVFGSTLNLFGKEFAKFGVE 132 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 + +D+A W+AA +PNTKL F E+P+NPL E+ DI ALA++AHA GALLAVDNCFC+ Sbjct: 133 TSFVSQTDIAQWQAAMRPNTKLLFAETPTNPLTEVCDIRALADVAHAGGALLAVDNCFCS 192 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVG-FLRTAGPTLSPFNA 258 PALQ+P +LGAD+VIHS TKY+DGQGR M G + G + + +V G +RTAG L+PFNA Sbjct: 193 PALQRPTELGADLVIHSGTKYLDGQGRVMAGAICGPSKLIVDVFGPIVRTAGMVLAPFNA 252 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGF-G 317 W+ LKG+ETLRIRMQA SA+ALA+A+WLE P + RVYY GLPSHPQHELA RQQSG G Sbjct: 253 WVVLKGMETLRIRMQAQSATALAIAQWLETHPAVTRVYYPGLPSHPQHELAMRQQSGLGG 312 Query: 318 AVVSFDVKGG-----RDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRAR 372 AVVSFDV+GG R A+ I++T++VSI TNLGDTK+ I HP TTSHGRL+ R Sbjct: 313 AVVSFDVRGGDPETARANAFHVINSTQVVSIATNLGDTKSIITHPGTTSHGRLTEAQRQA 372 Query: 373 AGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 AGI LIR A GLE +DDLKAD+ARGL +L Sbjct: 373 AGIKQGLIRFATGLEHIDDLKADLARGLDSL 403 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: 475 Number of extensions: 13 Number of successful extensions: 4 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