Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 3609021 Dshi_2410 O-succinylhomoserine sulfhydrylase (RefSeq)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Dino:3609021 Length = 392 Score = 367 bits (941), Expect = e-106 Identities = 188/385 (48%), Positives = 267/385 (69%), Gaps = 2/385 (0%) Query: 21 TLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGN-VYSRYTNPTVRTFE 79 T V AG RR+ GE EA+F T +V+ TA A ARF +Y+RY NPTVR FE Sbjct: 8 TKLVHAGTRRSQYGEVAEAIFLTQGFVYDTAEAAEARFIEAGADEFIYARYGNPTVRMFE 67 Query: 80 ERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQ 139 +RIAA+EG E A ATASGM+A+ + S+ +GDHV+ +R++FGS + + ++ R+G++ Sbjct: 68 DRIAAVEGTEDAFATASGMAAVNGALASMLRAGDHVVSARALFGSCLYILEEVLTRYGVE 127 Query: 140 VDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCT 199 V + +DLAAW AA +P+TK F E+ SNP E++DI A+A++AHA GAL+ VDN F T Sbjct: 128 VTFVDGTDLAAWRAAIRPDTKAVFFETISNPTLEVIDIEAVAKLAHAVGALVIVDNVFAT 187 Query: 200 PALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVV-GFLRTAGPTLSPFNA 258 P + GADV+++SATK+IDGQGR +GGV+ G + +++V +L+ G +LSPFNA Sbjct: 188 PIFSRAKDQGADVIVYSATKHIDGQGRCLGGVICGTRDFVRKVAEPYLKHTGGSLSPFNA 247 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318 W+ LK +ETL +R++A + +A ALAE LE +E+V + LPSHPQ++LAR Q + G Sbjct: 248 WVMLKSMETLDLRVRAQAETAQALAETLEGHAALEKVIFPHLPSHPQYDLARAQMAAGGT 307 Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378 V++ D+KGG+ A+RF++A +V+I+ NLGD K+ HPATT+H RL+PE RA GI D Sbjct: 308 VLALDIKGGKAGAFRFLNALEIVTISNNLGDAKSIATHPATTTHQRLTPEQRAGLGITDG 367 Query: 379 LIRVAVGLEDLDDLKADMARGLAAL 403 LIR++VGLED DL D+ LAA+ Sbjct: 368 LIRLSVGLEDAGDLLRDLQTALAAV 392 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: 344 Number of extensions: 7 Number of successful extensions: 3 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: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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 09 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