Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate GFF2301 PS417_11735 methionine gamma-lyase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__WCS417:GFF2301 Length = 411 Score = 295 bits (756), Expect = 1e-84 Identities = 160/389 (41%), Positives = 241/389 (61%), Gaps = 8/389 (2%) Query: 19 FDTLAVRAGQRRTPEGEHGEA---LFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTV 75 F T A+ G P+ HG ++ ++++ F TA AA FAGE G+ Y+R +NPT+ Sbjct: 10 FSTRAIHHGY--DPKDHHGALVPPIYLSATFAFPTAEYGAACFAGEASGHFYTRISNPTL 67 Query: 76 RTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKR 135 E R+A LE + AVA +SGM AI A +L GD V+VS++++G T +L Sbjct: 68 ALLESRMATLENGDAAVAFSSGMGAIAATFWTLLRPGDEVIVSQTLYGCTFALLHHGIGE 127 Query: 136 FGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAK-GALLAVD 194 FGI+V + L+DL A +AA P T++ + E+P+NP LVDIAA+A +AH + L VD Sbjct: 128 FGIKVRHVDLTDLTALQAALTPATRMIYCETPANPNLRLVDIAAVAALAHQQPNVTLVVD 187 Query: 195 NCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGE--QMKEVVGFLRTAGPT 252 N +CTP LQ+PL+LGADVV+HSATKY+ G G G+ Q + G G Sbjct: 188 NTYCTPYLQRPLELGADVVVHSATKYLSGHGDITAGIAVSNQALAQRIRLQGLKDLTGAV 247 Query: 253 LSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQ 312 +SP +A L ++GL+TL +RM H ++A A+AE L+ P ++ V Y GL S PQ+ELA +Q Sbjct: 248 MSPQDASLLMRGLKTLALRMDRHCSNAQAVAEALQAHPAVQSVTYPGLRSFPQYELATQQ 307 Query: 313 QSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRAR 372 G +++F++KGG + RF++A ++ + +LGD ++ HPA+ +H +P++RA Sbjct: 308 MKMPGGMIAFELKGGIETGRRFMNALKLFTRAVSLGDAESLAQHPASMTHSTYTPQERAA 367 Query: 373 AGIGDSLIRVAVGLEDLDDLKADMARGLA 401 GI + L+R++VGLED+ DL AD+ + LA Sbjct: 368 HGISEGLVRLSVGLEDVADLLADVQQALA 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: 396 Number of extensions: 13 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: 411 Length adjustment: 31 Effective length of query: 372 Effective length of database: 380 Effective search space: 141360 Effective search space used: 141360 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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