Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate GFF1863 HP15_1820 methionine gamma-lyase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Marino:GFF1863 Length = 413 Score = 526 bits (1356), Expect = e-154 Identities = 251/393 (63%), Positives = 317/393 (80%) Query: 11 DSDLEGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRY 70 +SDL+G + DTLAVRAGQ RT + EH +A+F TSS+V+ +AA AAARF GE PGN+YSR+ Sbjct: 13 ESDLDGMSVDTLAVRAGQIRTGQLEHSDAIFPTSSFVYGSAAQAAARFGGEEPGNIYSRF 72 Query: 71 TNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFD 130 TNPTV+ FE RIAA+EG E+AVATASGMSAIL+ M+L SGDHV+ SR VFG+T LF Sbjct: 73 TNPTVQAFEGRIAAMEGGERAVATASGMSAILSTCMALLKSGDHVICSRGVFGTTNVLFQ 132 Query: 131 KYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGAL 190 KY RFG++ + L+D+ W+A+ + T++ F+E+PSNPL E+ D+ L ++A AL Sbjct: 133 KYMARFGVETTFVSLTDMEEWQASIRSETRMLFIETPSNPLCEVADMEILGQLARDNDAL 192 Query: 191 LAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAG 250 VDNCFCTP LQ+PL+ GAD+VIHSATKY+DGQGR +GGVV G + M+EV GFLR+AG Sbjct: 193 FVVDNCFCTPVLQRPLEQGADIVIHSATKYLDGQGRCVGGVVVGSEKMMEEVYGFLRSAG 252 Query: 251 PTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELAR 310 PT+SPFNAW+F KGLETL IRM+AH +AL LA WLE+QP +ERV+YAGL SHPQHELA+ Sbjct: 253 PTMSPFNAWVFQKGLETLPIRMRAHCDNALELALWLEQQPAVERVFYAGLQSHPQHELAK 312 Query: 311 RQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDR 370 +QQ+GFG V+SF +KG R+ AWRFID TRM+SIT NLGD KTTI HPATT+HGRLSPED+ Sbjct: 313 KQQTGFGGVLSFQLKGAREEAWRFIDGTRMISITANLGDVKTTITHPATTTHGRLSPEDK 372 Query: 371 ARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 ARAGI ++LIR++VG+E ++DLK D+ RG AL Sbjct: 373 ARAGITENLIRISVGIEAVEDLKTDLERGFQAL 405 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: 474 Number of extensions: 17 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: 413 Length adjustment: 31 Effective length of query: 372 Effective length of database: 382 Effective search space: 142104 Effective search space used: 142104 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