Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 200974 SO1812 methionine gamma-lyase (NCBI ptt file)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__MR1:200974 Length = 397 Score = 328 bits (841), Expect = 2e-94 Identities = 171/384 (44%), Positives = 238/384 (61%), Gaps = 1/384 (0%) Query: 21 TLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEE 80 T A+ AG R G L+ T+++VF +A RFAG PG +Y+R NPTV E Sbjct: 13 TQAIHAGHEREAFGSLVTPLYQTATFVFDSAQQGGERFAGNEPGYIYTRLGNPTVAELER 72 Query: 81 RIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQV 140 ++A LE AE A ATASGM A+ A +++ GDH++ S +V+G T +L F RFGI+V Sbjct: 73 KMAILERAEAAAATASGMGAVSAALLANLQIGDHLVASNAVYGCTFALMTNQFARFGIEV 132 Query: 141 DYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTP 200 SD+ E A KPNTK+ F E+P NP ++ D++A+A IA VDN F TP Sbjct: 133 TLVDFSDVELIERAIKPNTKVIFCETPVNPHLQVFDLSAIAAIAKRHSLTSIVDNTFMTP 192 Query: 201 ALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEV-VGFLRTAGPTLSPFNAW 259 LQQP+ LG DVV+HSATKY++G G + G+V G Q+ V L+ G +SP +AW Sbjct: 193 LLQQPIALGIDVVVHSATKYLNGHGDVIAGIVCGSEAQLHRVKYEILKDIGAVMSPHDAW 252 Query: 260 LFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAV 319 L L+GL+TL +R+Q H SA +AE+LE+ P + RVYY GL SH H +Q G V Sbjct: 253 LILRGLKTLDVRLQRHCESAQRVAEFLEQHPAVTRVYYPGLKSHSGHRFIGQQMRRAGGV 312 Query: 320 VSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSL 379 ++F++ A F+ ++ SI +LGD ++ I HPA+ +H SPE RA AGIGD+L Sbjct: 313 IAFELAADFTQAMAFVGNLKLFSIAVSLGDAESLIQHPASMTHSPYSPEARAAAGIGDNL 372 Query: 380 IRVAVGLEDLDDLKADMARGLAAL 403 +R++VGLED DD+ AD+++ LAAL Sbjct: 373 LRISVGLEDCDDIIADLSQALAAL 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: 355 Number of extensions: 15 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: 397 Length adjustment: 31 Effective length of query: 372 Effective length of database: 366 Effective search space: 136152 Effective search space used: 136152 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