Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate PP_1308 PP_1308 methionine gamma-lyase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Putida:PP_1308 Length = 398 Score = 301 bits (772), Expect = 2e-86 Identities = 156/373 (41%), Positives = 238/373 (63%), Gaps = 6/373 (1%) Query: 36 HGEAL----FTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQA 91 HG AL + T++Y F T AA FAGE PG+ YSR +NPT+ E+R+A+LEG E Sbjct: 24 HGGALVPPVYQTATYAFPTVEYGAACFAGEEPGHFYSRISNPTLALLEQRMASLEGGEAG 83 Query: 92 VATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAW 151 +A ASGM AI + + +L GD ++V R+++G T + FG++V + L+D A Sbjct: 84 LALASGMGAITSTLWTLLRPGDELIVGRTLYGCTFAFLHHGIGEFGVKVRHVDLNDAKAL 143 Query: 152 EAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGAD 211 +AA T++ + E+P+NP +LVDIAA+ E + VDN +CTP LQ+PL+LGAD Sbjct: 144 KAAISSKTRMIYFETPANPNMQLVDIAAVVEAVRGHDVHVVVDNTYCTPYLQRPLELGAD 203 Query: 212 VVIHSATKYIDGQGRGMGGVVAGRGEQMKEV--VGFLRTAGPTLSPFNAWLFLKGLETLR 269 +V+HSATKY+ G G G+V GR + + G G LSP +A L ++G++TL Sbjct: 204 LVVHSATKYLSGHGDITAGLVVGRKVLVDRIRLEGLKDMTGAVLSPHDAALLMRGIKTLA 263 Query: 270 IRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVSFDVKGGRD 329 +RM H A+A +AE+L RQP +E ++Y GLPS Q+ LA+RQ G +++F++KGG + Sbjct: 264 LRMDRHCANAQQVAEFLVRQPQVELIHYPGLPSFAQYALAQRQMRLPGGMIAFELKGGIE 323 Query: 330 AAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDL 389 A RF++A ++ + +LGD ++ HPA+ +H +P++RA GI + L+R++VGLED+ Sbjct: 324 AGRRFMNALQLFARAVSLGDAESLAQHPASMTHSSYTPQERAHHGISEGLVRLSVGLEDV 383 Query: 390 DDLKADMARGLAA 402 +DL AD+ + L A Sbjct: 384 EDLLADVEQALQA 396 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: 374 Number of extensions: 10 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: 398 Length adjustment: 31 Effective length of query: 372 Effective length of database: 367 Effective search space: 136524 Effective search space used: 136524 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