Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_086510355.1 BZY95_RS13035 methionine gamma-lyase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_002151265.1:WP_086510355.1 Length = 415 Score = 343 bits (880), Expect = 5e-99 Identities = 179/389 (46%), Positives = 248/389 (63%), Gaps = 3/389 (0%) Query: 15 EGAAFDTLAVRAG-QRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNP 73 +G F T A+ A R +G + TS++ F + A RFAGE PG+ YSR +NP Sbjct: 23 QGQGFATRAIHAAYDSRDEQGALTPPMHLTSTFTFESVEQGAERFAGEAPGHFYSRISNP 82 Query: 74 TVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYF 133 TV T E+R+A LEGAE +ATASGM AI AL+ SL GD ++ ++G T + F Sbjct: 83 TVATLEQRMANLEGAEAGLATASGMGAITALMWSLLRPGDELITDSHLYGCTHAFFHHGL 142 Query: 134 KRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAV 193 FGI+V + LS AA E A TKL + E+P+NP LVDI A++ IAH GA + V Sbjct: 143 TEFGIRVKHVDLSQPAALEVAIGERTKLVYFETPANPTMRLVDIEAVSRIAHRHGARVVV 202 Query: 194 DNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEV--VGFLRTAGP 251 DN + TP + +P++ GAD V+HSATKY+ G G + GV+ G + + V G G Sbjct: 203 DNTYATPVITRPIEQGADFVVHSATKYLGGHGDLIAGVLVGSVDDIHRVRLTGLKDFTGA 262 Query: 252 TLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARR 311 +SPF A+L ++GL+TL IRMQ SASAL +A WLER P +ERV+Y GL S PQHELARR Sbjct: 263 VMSPFTAFLIMRGLKTLEIRMQRQSASALEVARWLERHPAVERVHYPGLTSFPQHELARR 322 Query: 312 QQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRA 371 Q S +G +++F++ GG +A RF++ ++ +LGD ++ I HPA+ +H LSPE+RA Sbjct: 323 QMSDYGGIIAFELAGGLEAGRRFMNRLELIQRAVSLGDAESLIQHPASMTHSVLSPEERA 382 Query: 372 RAGIGDSLIRVAVGLEDLDDLKADMARGL 400 GI ++LIR++VGLE DL+AD+A+ L Sbjct: 383 EHGISETLIRLSVGLETPSDLRADLAQAL 411 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: 399 Number of extensions: 13 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: 415 Length adjustment: 31 Effective length of query: 372 Effective length of database: 384 Effective search space: 142848 Effective search space used: 142848 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