Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate PP_0659 PP_0659 Cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Putida:PP_0659 Length = 423 Score = 276 bits (705), Expect = 1e-78 Identities = 143/344 (41%), Positives = 210/344 (61%) Query: 60 GEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSR 119 G+ PG +YSR +NPTV T E ++A LE AE AVA +SGM+AI A++ + S+G V+ +R Sbjct: 57 GKQPGFIYSRMSNPTVATLEAKLAELEQAESAVAFSSGMAAISAVLHTFLSNGKRVVSTR 116 Query: 120 SVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAA 179 +G T +F+++ R G+QV D A E L ++E+P+NP +++DI Sbjct: 117 DSYGGTNKIFEEFLPRMGVQVCLCDTLDTEALEREIAAGCDLLYLETPTNPTLKVLDIRR 176 Query: 180 LAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQM 239 L+ AH GAL+ DN F TP Q PL LG DVV+HSATK++ G G +GGVV G M Sbjct: 177 LSAAAHKVGALVVADNTFATPLNQNPLALGVDVVVHSATKFLSGHGDVLGGVVCGAEALM 236 Query: 240 KEVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAG 299 +V + G L PF+A+L ++G++TL +R++ ASA+ALA +L +P +E V Y G Sbjct: 237 AQVRHYREINGAALDPFSAYLIIRGIKTLAVRLRQQQASAMALAHYLSTEPLVEAVNYPG 296 Query: 300 LPSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPAT 359 LP+H H +A+ Q GFGA+VSF +KGG R + + NLG +T T Sbjct: 297 LPAHAGHAIAKAQMRGFGAIVSFVLKGGMPTVARLLPRLKYAHRAGNLGAVETIYGPART 356 Query: 360 TSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 TSH + E+R GI + L+R++VG+E+ DDL AD+A+ A++ Sbjct: 357 TSHVENTLEERLALGISEGLVRISVGIEETDDLLADLAQACASV 400 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: 380 Number of extensions: 11 Number of successful extensions: 1 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: 423 Length adjustment: 31 Effective length of query: 372 Effective length of database: 392 Effective search space: 145824 Effective search space used: 145824 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