Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 203140 SO4056 cystathionine gamma-synthase (NCBI ptt file)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__MR1:203140 Length = 393 Score = 254 bits (649), Expect = 3e-72 Identities = 139/338 (41%), Positives = 203/338 (60%), Gaps = 2/338 (0%) Query: 67 YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126 YSR NPT + +A LE V T +GM+AI LV +L D ++V +G + Sbjct: 53 YSRSGNPTRSILGDALAKLEKGATGVVTCTGMAAI-TLVTTLLGPDDLLVVPHDCYGGSY 111 Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186 LF K+ ++ +D A A K+ ++E+PSNPL +VDI A+A+ +H Sbjct: 112 RLFTNLAKKGQFKLLVVDQTDNQALAQAIAQQPKMVWIETPSNPLLRVVDIEAIAKASHG 171 Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFL 246 GAL+ VDN F +P LQQPL LGAD+VIHS TKYI+G +GG V + Q+ E + + Sbjct: 172 VGALVVVDNTFLSPILQQPLLLGADIVIHSTTKYINGHSDVVGGAVIAKDPQIGETLHWW 231 Query: 247 -RTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQ 305 T G T S F+++ L+GL TL +R++ H +A + E L P + +VYY GL HP Sbjct: 232 SNTLGLTGSAFDSYQTLRGLRTLAVRIREHQRNAQRIVELLSNSPVVSKVYYPGLADHPG 291 Query: 306 HELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRL 365 H +A +QQ GFGA++SF++KGG F+DA + S+ +LG ++ +A PAT +H + Sbjct: 292 HAIAAKQQKGFGAMLSFELKGGEAEVVAFLDALSLFSVAESLGGVESLVAVPATMTHRAM 351 Query: 366 SPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 P+ R AGI D+L+R++VG+ED DDL AD+ GLAA+ Sbjct: 352 EPQARFEAGIKDTLLRLSVGIEDADDLVADIQAGLAAV 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: 344 Number of extensions: 16 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: 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