Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Dsui_2042 Dsui_2042 cystathionine beta-lyase/cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__PS:Dsui_2042 Length = 392 Score = 282 bits (722), Expect = 1e-80 Identities = 164/389 (42%), Positives = 237/389 (60%), Gaps = 11/389 (2%) Query: 19 FDTLAVRAGQRRTPE-GEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 F T A+ AGQ P G ++ TS+YV + A + ++AG Y+R NPT Sbjct: 7 FATRAIHAGQEPDPTTGAVSIPIYATSTYV-QPALNEPKQYAGATFD--YARSANPTRLA 63 Query: 78 FEERIAALEGAEQAVAT----ASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYF 133 E IA LEG A AT ASG++A A V+ L +G HV+ S ++G ++ LF++ Sbjct: 64 LERCIADLEGGAFATATGFAFASGLAAS-ATVLELLPAGSHVVASDDLYGGSVRLFNRVR 122 Query: 134 KRFG-IQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLA 192 ++V Y S + EAA P TKL +VE+PSNPL +LVD+ +A I +G L Sbjct: 123 SNSADLKVTYADFSSRESIEAAITPETKLLWVETPSNPLLKLVDLDLVAAIGKDRGLLTV 182 Query: 193 VDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-GP 251 DN F +P +Q+PL+ G D+V+HSATKY++G + GV + E + FL+ A G Sbjct: 183 ADNTFASPWIQRPLEHGFDIVVHSATKYLNGHSDVIAGVAVTARADLAERLAFLQNAAGA 242 Query: 252 TLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARR 311 L PF+A+L L+GL+TL +RM+ H A+A A+A WLE+ P IE+V+Y GL SHPQHELA+R Sbjct: 243 VLGPFDAFLALRGLKTLALRMERHCANAEAIARWLEQHPAIEKVHYPGLASHPQHELAKR 302 Query: 312 QQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRA 371 Q GFG +VS VKGG AA + ++ T++ + +LG ++ I PA +H + PE R Sbjct: 303 QMRGFGGMVSAVVKGGLPAAKKLLENTKIFVLAESLGGVESLIELPALMTHASVPPEQRR 362 Query: 372 RAGIGDSLIRVAVGLEDLDDLKADMARGL 400 R GI D L+R++VG+ED++DL AD+ + L Sbjct: 363 RIGIDDGLVRLSVGVEDVEDLLADLEQAL 391 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: 393 Number of extensions: 12 Number of successful extensions: 4 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