Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate CA265_RS08190 CA265_RS08190 cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Pedo557:CA265_RS08190 Length = 371 Score = 215 bits (547), Expect = 2e-60 Identities = 121/350 (34%), Positives = 200/350 (57%), Gaps = 15/350 (4%) Query: 53 DAAARFAGEVPGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSG 112 DA + G G++YSR +NP E +A LE E A A +SG + L L +L G Sbjct: 34 DAEGGYPG---GHMYSRVSNPNRSALENTVAKLEYGEDAAAFSSGNTCGLVLFQAL-KPG 89 Query: 113 DHVLVSRSVFGSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLA 172 H++ ++ F ++ D+ +DL +A+ + NTKL ++E+PSNPL Sbjct: 90 SHIIAPDDMYWGIKKQLLTIFND-SLEFDFIDQTDLDLIQASIRSNTKLIWIETPSNPLL 148 Query: 173 ELVDIAALAEIAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVV 232 ++ DI +A+IA AK LA D+ F +P LQ P+ LGAD+V+HS+TKY+ G +GG++ Sbjct: 149 KVTDIEEIAKIAKAKNITLACDSTFASPILQNPILLGADIVMHSSTKYLGGHSDVLGGIL 208 Query: 233 --AGRGEQMKEVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQP 290 A + E +++ +T G SPF+ +L + ++TL RM+ H + +A++L P Sbjct: 209 VTAKKDELWEKIKNIQQTGGAVPSPFDCFLLTRSIKTLAYRMKGHCENGKIIADYLNAHP 268 Query: 291 GIERVYYAGLPSHPQHELARRQQSGFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDT 350 +E V+Y GL SHPQH++A++Q FG ++SF VKG +AA + ++ ++ + T+LG Sbjct: 269 NVEAVFYPGLESHPQHDIAKKQMKDFGGMMSFLVKGDVEAAHKVVNKVQLFAQATSLGGV 328 Query: 351 KTTIAHPATTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGL 400 ++ I H + P+ + +L+R++VGLE DD+ AD+A+ L Sbjct: 329 ESLIEHRYSVE----GPDSKT----PKNLLRISVGLEHADDIIADLAQAL 370 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: 319 Number of extensions: 12 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: 371 Length adjustment: 30 Effective length of query: 373 Effective length of database: 341 Effective search space: 127193 Effective search space used: 127193 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