Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 5208004 Shew_0520 O-succinylhomoserine (thiol)-lyase (RefSeq)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__PV4:5208004 Length = 388 Score = 257 bits (656), Expect = 5e-73 Identities = 141/337 (41%), Positives = 207/337 (61%), Gaps = 2/337 (0%) Query: 67 YSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTI 126 YSR NPT + IA LE V T +GM+AI LV SL D ++V +G + Sbjct: 47 YSRSGNPTRSILGDAIAELEQGATGVVTCTGMAAI-TLVTSLLGPEDLLVVPHDCYGGSY 105 Query: 127 SLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHA 186 LF K+ ++ +D A E A + K+ ++E+PSNPL +VDI A+A+ +H Sbjct: 106 RLFTNLAKKGAFKLLVVDQTDERALEQALTQSPKMVWLETPSNPLLRVVDIEAIAQASHK 165 Query: 187 KGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFL 246 GA + VDN F +P LQQPL+LGAD+V+HS TKYI+G +GG V + ++ E++ + Sbjct: 166 VGAQVVVDNTFLSPVLQQPLQLGADIVVHSTTKYINGHSDVVGGAVVAKDPEVGELLHWW 225 Query: 247 -RTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQ 305 T G T S F+++L L+GL TL +R++ H A+A + L +E+VYY GL HP Sbjct: 226 SNTLGLTGSAFDSYLTLRGLRTLAVRIREHQANAQKVLALLCDHKAVEKVYYPGLAEHPG 285 Query: 306 HELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRL 365 HE+A RQQ GFGA++SF++KGG A F+DA + S+ +LG ++ +A PAT +H + Sbjct: 286 HEIAARQQKGFGAMLSFELKGGESALVAFLDALQYFSVAESLGGVESLVAVPATMTHRAM 345 Query: 366 SPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAA 402 P+ R AG+ D+LIR++VG+ED +DL AD+ GL A Sbjct: 346 DPDARREAGVKDTLIRLSVGIEDGEDLVADILAGLEA 382 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: 361 Number of extensions: 17 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: 388 Length adjustment: 31 Effective length of query: 372 Effective length of database: 357 Effective search space: 132804 Effective search space used: 132804 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