Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Pf1N1B4_4890 Cystathionine gamma-lyase (EC 4.4.1.1)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4890 Length = 393 Score = 305 bits (780), Expect = 2e-87 Identities = 164/386 (42%), Positives = 247/386 (63%), Gaps = 13/386 (3%) Query: 19 FDTLAVRAGQRRTPE-GEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 F T + AGQ P G ++ S+Y+ ++ G G Y R NPT Sbjct: 13 FATRVIHAGQTPDPSTGALMPPIYANSTYLQQSP--------GVHKGFDYGRSHNPTRFA 64 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRF- 136 E +A LEG +A A ASG++AI A V+ L +G H++ ++G T LFDK +R Sbjct: 65 LERCVADLEGGTRAFAFASGLAAI-ANVLELLDAGAHIVSGNDLYGGTFRLFDKVRRRSA 123 Query: 137 GIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNC 196 G + + L+DLAA+EAA + +T++ +VE+PSNPL L D+ A+A I +G + DN Sbjct: 124 GHRFSFVDLTDLAAFEAALEDDTRMVWVETPSNPLLSLTDLDAVARICRQRGIICVADNT 183 Query: 197 FCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGV-VAGRGEQMKEVVGFLRTA-GPTLS 254 F +P +Q+PL+LG D+V+HS TKY++G +GG+ V G+ ++ E +GFL+ A G Sbjct: 184 FASPWIQRPLELGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELAERLGFLQNAVGAIAG 243 Query: 255 PFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQS 314 PF+A+L L+G++TL +RM+ H ++AL LA+WLERQP + RVYY GLPSHPQHELARRQ Sbjct: 244 PFDAFLTLRGVKTLALRMERHCSNALELAQWLERQPQVARVYYPGLPSHPQHELARRQMR 303 Query: 315 GFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAG 374 GFG ++S D+ A RF+++ R+ ++ +LG ++ I HPA +H + E RA+ G Sbjct: 304 GFGGMISLDLNSDLAGAKRFLESVRIFALAESLGGVESLIEHPAIMTHASIPVETRAQLG 363 Query: 375 IGDSLIRVAVGLEDLDDLKADMARGL 400 IGD+L+R++VG+ED++DL+AD+A+ L Sbjct: 364 IGDALVRLSVGVEDVEDLRADLAQAL 389 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: 414 Number of extensions: 23 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: 393 Length adjustment: 31 Effective length of query: 372 Effective length of database: 362 Effective search space: 134664 Effective search space used: 134664 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