Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate CA265_RS06375 CA265_RS06375 cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Pedo557:CA265_RS06375 Length = 379 Score = 256 bits (653), Expect = 1e-72 Identities = 139/386 (36%), Positives = 226/386 (58%), Gaps = 12/386 (3%) Query: 19 FDTLAVRAGQRRTPE-GEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 F T A+ AGQ P G ++ TS+Y ++ G+ G YSR TNPT + Sbjct: 3 FATKAIHAGQEPDPTTGAVMTPIYQTSTYWQKSP--------GDNKGYEYSRGTNPTRKA 54 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFG 137 E+ +AALE A+ +A +SGM A A V+ L GD V+ ++G + +F K F ++G Sbjct: 55 LEDCLAALENAKYGLAFSSGMGATDA-VLKLLQPGDEVITGNDLYGGSYRIFTKIFTKYG 113 Query: 138 IQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCF 197 I+ + LS TKL ++E+P+NP +++DI +A+I K +L VDN F Sbjct: 114 IKFHFLDLSKPENILPYINDKTKLVWIETPTNPTMQIIDIEGVAKITKEKNLILTVDNTF 173 Query: 198 CTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-GPTLSPF 256 +P LQ P+ LGAD+V+HS TKYI G + G + EQ+ + + F+ A G T P Sbjct: 174 ASPYLQNPIDLGADIVMHSVTKYIGGHSDVVMGALVTNDEQLYKDLWFIYNACGATPGPQ 233 Query: 257 NAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGF 316 +A+L L+G++TL +RM+AH + +A +L+ P ++++Y+ G HP H++A++Q GF Sbjct: 234 DAFLVLRGIKTLHLRMKAHCENGERIAHYLKTHPKVDKIYWPGFEDHPNHDIAKKQMRGF 293 Query: 317 GAVVSFDVKGG-RDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGI 375 G ++S +KG + +R ++ ++ +LG ++ I HPAT +HG + E+R + G+ Sbjct: 294 GGMISITLKGADLEETFRISSNFKVFTLAESLGGVESLINHPATMTHGSIPKEEREKVGV 353 Query: 376 GDSLIRVAVGLEDLDDLKADMARGLA 401 D+L+R++VG+ED+DDL D+A LA Sbjct: 354 TDNLLRLSVGVEDIDDLLEDLANALA 379 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: 365 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: 379 Length adjustment: 31 Effective length of query: 372 Effective length of database: 348 Effective search space: 129456 Effective search space used: 129456 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