Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 6937071 Sama_1242 methionine gamma-lyase (RefSeq)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__SB2B:6937071 Length = 392 Score = 315 bits (806), Expect = 2e-90 Identities = 163/390 (41%), Positives = 241/390 (61%), Gaps = 1/390 (0%) Query: 15 EGAAFDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPT 74 E + TL V G R G L+ ++++VF A ARFAG+ G +Y+R NPT Sbjct: 3 EKSKLATLVVHGGHERDAMGALVSPLYQSATFVFDNARQGGARFAGDEAGYIYTRLGNPT 62 Query: 75 VRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFK 134 E ++A LEGAE+A ATASGM A+ A +++ S GDH++ SR+V+G T +L Sbjct: 63 TAELERKLAILEGAEEAAATASGMGAVSAALLANLSQGDHLVASRAVYGCTFALMTDLMA 122 Query: 135 RFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVD 194 RFGI+V + AA EAA + NT+ F E+P NP ++ D+ A+A I G L VD Sbjct: 123 RFGIEVTLVDFKEPAAIEAAIRDNTRAIFCETPVNPHLDVFDLDAIAAIGKRHGLLTIVD 182 Query: 195 NCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEV-VGFLRTAGPTL 253 N F TP LQ+PL G D+VIHSATKY++G G + G+VAG EQ+ +V ++ G + Sbjct: 183 NTFMTPLLQRPLDHGIDMVIHSATKYLNGHGDVIAGMVAGSKEQIDKVKYQIIKDIGAVM 242 Query: 254 SPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQ 313 SP +AWL L+G++TL +R+Q H +A +A++LE P + RVYY L SH H Q Sbjct: 243 SPHDAWLILRGMKTLDVRVQRHCDNAEKIADFLEAHPRVGRVYYPALKSHQGHRFLGTQM 302 Query: 314 SGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARA 373 G V++F++K + + F+D+ ++ +I +LGD ++ I HPA+ +H +PE R A Sbjct: 303 RRAGGVIAFELKSDIEGSINFVDSLKVFTIAVSLGDAESLIQHPASMTHSPYTPEARLEA 362 Query: 374 GIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 GI D+L+R++VGLED+DDL AD+++ LA + Sbjct: 363 GITDTLLRISVGLEDVDDLIADLSQALAKI 392 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: 359 Number of extensions: 11 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: 392 Length adjustment: 31 Effective length of query: 372 Effective length of database: 361 Effective search space: 134292 Effective search space used: 134292 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