Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_029134534.1 A3GO_RS0117690 methionine gamma-lyase
Query= SwissProt::P55218 (403 letters) >NCBI__GCF_000428045.1:WP_029134534.1 Length = 398 Score = 310 bits (793), Expect = 6e-89 Identities = 168/386 (43%), Positives = 237/386 (61%), Gaps = 3/386 (0%) Query: 19 FDTLAVRAG-QRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 F T A+ G +G ++ +S+Y F T AD +ARFAGE G VYSR NPT Sbjct: 11 FSTRAIHHGYDAYAGDGALNPPVYMSSTYTFPTVADGSARFAGEQAGYVYSRVGNPTTAL 70 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFG 137 E+RIA LEG E A+ T SGM A +L+ +L GD V+ ++++G T + F+ RFG Sbjct: 71 LEQRIADLEGGEAALVTGSGMGATASLLWTLLKPGDEVIADKTLYGCTYAYFNHGLARFG 130 Query: 138 IQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCF 197 +++ + L++ A T+L F ESP+NP LVDIAA+A IA + A + VDN + Sbjct: 131 VKITHVDLTEPDNLSRAISGKTRLVFFESPANPNMRLVDIAAVAAIARSHDAKVVVDNTY 190 Query: 198 CTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEV--VGFLRTAGPTLSP 255 CTP LQ+PL+LGAD V+HSATKY+ G G + G + G E + EV G G LS Sbjct: 191 CTPYLQRPLELGADYVVHSATKYLGGHGDLIAGAIVGPKESLDEVRFYGLKDMTGAVLSS 250 Query: 256 FNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSG 315 +A+L L+GL+TL +RM H +A +AE+L P +E ++ GL S PQ ELA RQ S Sbjct: 251 QDAFLILRGLKTLALRMDRHCQNAQGIAEFLADHPKVEVCHFPGLVSFPQRELAERQMSA 310 Query: 316 FGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGI 375 G +V+FD+KGG +A RF+DA ++V+ +LGD ++ HPA+ +H +PE+RA I Sbjct: 311 PGGMVAFDLKGGLEAGCRFMDALQLVTRAVSLGDAESLAQHPASMTHSVYTPEERAAHLI 370 Query: 376 GDSLIRVAVGLEDLDDLKADMARGLA 401 + L+R++ GLEDLDDL D+ R LA Sbjct: 371 SEGLVRLSAGLEDLDDLLGDIDRALA 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: 389 Number of extensions: 15 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: 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 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