Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Dsui_0429 Dsui_0429 cystathionine beta-lyase/cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__PS:Dsui_0429 Length = 382 Score = 183 bits (464), Expect = 8e-51 Identities = 120/344 (34%), Positives = 183/344 (53%), Gaps = 16/344 (4%) Query: 64 GNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFG 123 G VYSR +P E + LEG A ASGM+A A++ +L G V+ R+++ Sbjct: 51 GRVYSRDGSPAYDGPEALLKELEGGAAAALFASGMAAASAVLQAL-KPGARVVAPRAMYW 109 Query: 124 STISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEI 183 + + ++ + + +++ +D A A + L ++E+P+NP E+ DIAA A+ Sbjct: 110 ALRNWMIQFAANWQLTLEF--FADDAELAALLQRPADLVWLETPANPTWEITDIAAAAKA 167 Query: 184 AHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQ--MKE 241 AHA GA L VD+ TP +PL+LGADVV+HSATKY++G + G + R E + Sbjct: 168 AHAAGARLVVDSTVPTPVFTRPLELGADVVMHSATKYLNGHSDVVAGALVTRTEDDFWQR 227 Query: 242 VVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLP 301 + G L PF AWL +G+ TL R++ +ASA A+A + V Y GLP Sbjct: 228 IKTVRALGGAVLGPFEAWLLARGMRTLFPRVRTAAASAAAIASHFHGHAKVGLVLYPGLP 287 Query: 302 SHPQHELARRQ-QSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATT 360 SHP H +A RQ Q GFGA++S + GG AA ++ T+LG ++ + H A+ Sbjct: 288 SHPGHAVAARQMQGGFGAMLSLRIAGGEAAAKAVAARLQVFQRATSLGSVESLVEHRASV 347 Query: 361 -SHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGLAAL 403 G P+D L+R++VG+E DL AD+ + LA + Sbjct: 348 EGPGTFCPDD---------LLRLSVGIEATADLIADLEQALAGV 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: 382 Number of extensions: 17 Number of successful extensions: 5 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: 382 Length adjustment: 31 Effective length of query: 372 Effective length of database: 351 Effective search space: 130572 Effective search space used: 130572 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