Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate SMc01976 SMc01976 hypothetical protein
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Smeli:SMc01976 Length = 390 Score = 221 bits (562), Expect = 4e-62 Identities = 135/365 (36%), Positives = 199/365 (54%), Gaps = 16/365 (4%) Query: 43 TSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAIL 102 TS + F+ + A + GE +Y+R NPTVR FEE +A LEGAE A+ ASGMSAI Sbjct: 33 TSLFTFKDYDEMVASYRGERVRPIYTRGLNPTVRHFEEMLAKLEGAEDAIGFASGMSAIS 92 Query: 103 ALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLF 162 + V+S GD ++ + V+ LF + KR ++V Y D A A P KLF Sbjct: 93 STVLSFVEPGDRIVAVKHVYPDAFRLFGTHLKRMRVEVTYVDGRDEEA-VAKALPGAKLF 151 Query: 163 FVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYID 222 ++ESP++ + + D+AALA +A +G + +DN + +P QQP+ LG D+VIHSA+KY+ Sbjct: 152 YMESPTSWVMDTHDVAALAALARRQGIVTVIDNSWASPVFQQPVSLGVDLVIHSASKYLG 211 Query: 223 GQGRGMGGVVAGRGEQMKEVVGFLRT-----AGPTLSPFNAWLFLKGLETLRIRMQAHSA 277 G + GVVAG G E++G +R+ G LSPF+AWL ++G+ TL +RM+AH Sbjct: 212 GHSDVVAGVVAGSG----ELIGRIRSEAYPYLGGKLSPFDAWLLIRGMRTLPVRMKAHER 267 Query: 278 SALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDA 337 SALA+A L P +E V + GL +H L SG + SF + G D RF D Sbjct: 268 SALAVARRLAEHPLVETVCHPGLGNHLPPGL-----SGTSGLFSFIFREGVDVR-RFADH 321 Query: 338 TRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMA 397 ++ + + G ++ I + P A GI +R+ VGLE + L +D+ Sbjct: 322 LKLFKLGVSWGGHESLIVPGEVVLAQKAEPNSAAAFGISPRSVRLHVGLEGTEALWSDLE 381 Query: 398 RGLAA 402 + A Sbjct: 382 AAMTA 386 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: 377 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: 390 Length adjustment: 31 Effective length of query: 372 Effective length of database: 359 Effective search space: 133548 Effective search space used: 133548 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