Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Echvi_2283 Echvi_2283 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Cola:Echvi_2283 Length = 391 Score = 381 bits (979), Expect = e-110 Identities = 184/382 (48%), Positives = 258/382 (67%) Query: 19 FDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTF 78 F+T AVR ++ + EH ++ TSS+ F +A +A FA E+PGN+YSRY NP Sbjct: 6 FETEAVRIASSKSNQREHSAPIYMTSSFTFDSAEEARQMFAEEIPGNIYSRYANPNSSDL 65 Query: 79 EERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGI 138 E++ A+EG E +ATASGM+A+ + SL GDH+L SRS+FGST L + F ++GI Sbjct: 66 IEKVCAVEGTEDGIATASGMAAMFGSMASLLEQGDHILASRSLFGSTHQLLTRVFPKWGI 125 Query: 139 QVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFC 198 Y +SD+ W+ KPNTK+ F+E+PSNP E++D+ + + A A +L VDNCF Sbjct: 126 TSTYGDISDIENWDKLVKPNTKMLFIETPSNPGLEVIDLEWIGKFAKAHNLILVVDNCFA 185 Query: 199 TPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSPFNA 258 TP LQQP K GAD+V HSATKYIDGQGR +GG++ G+ E +KEV F R GP++SPFNA Sbjct: 186 TPYLQQPAKWGADIVAHSATKYIDGQGRVLGGLILGKQELIKEVQFFTRHTGPSISPFNA 245 Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318 W+ + +ETL IRM+ H A+ALA+A + + +E V Y L SHPQH+LA++Q G Sbjct: 246 WILSRSMETLAIRMERHCANALAVASYFQDNKELEFVKYPFLKSHPQHDLAKKQMKHGGG 305 Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378 +V+ +KGG + A RFID +M+++T NLGDT++ I HPA+T+H +L+ E+R R GI Sbjct: 306 IVTLTLKGGIERAQRFIDELQMITVTANLGDTRSIITHPASTTHSKLTEEERQRVGILPG 365 Query: 379 LIRVAVGLEDLDDLKADMARGL 400 LIR++ GLE DD+ AD+ R L Sbjct: 366 LIRLSAGLEHHDDIIADIERAL 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: 360 Number of extensions: 10 Number of successful extensions: 1 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 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