Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate PP_4594 PP_4594 putative Cystathionine gamma-synthase
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Putida:PP_4594 Length = 393 Score = 263 bits (672), Expect = 7e-75 Identities = 157/388 (40%), Positives = 224/388 (57%), Gaps = 12/388 (3%) Query: 19 FDTLAVRAGQR-RTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRT 77 F T + AG++ + A+ T SS+ R+ D P YSR NPT Sbjct: 12 FATRTIHAGEQFSVADNAIFPAIVTASSFTKRSLDDK--------PEYSYSRVGNPTRHA 63 Query: 78 FEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRF- 136 +E +AALE AVA ASG++A A V+ L HV+V V+G T + + Y R Sbjct: 64 YETCVAALEEGVGAVACASGVNAT-ATVLELLPKDAHVVVMNGVYGGTFRIMEDYRSRTS 122 Query: 137 GIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNC 196 G+ Y L+D+ A AA KP T+L ++ESP+NPL LVDI A+ ++A AKG L +DN Sbjct: 123 GLTTTYVDLNDIEAVAAAIKPETQLIWIESPTNPLLHLVDIKAVCDLAKAKGILTCIDNT 182 Query: 197 FCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-GPTLSP 255 FC+P Q+P+ LG D+V+HSA+KYI G GGVV + + + + A G P Sbjct: 183 FCSPWNQRPITLGVDLVMHSASKYIGGHSDLTGGVVVAANDALLARLRRISMAIGAVQGP 242 Query: 256 FNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSG 315 F+ +L L+GL+TL +RM+ A+AL +A +LE +E+VYY GL SHPQHEL +RQ Sbjct: 243 FDCYLALRGLKTLDVRMERQCANALQVARFLEGHAQVEQVYYPGLESHPQHELCKRQMRS 302 Query: 316 FGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGI 375 GAVV+ VKG R A R ++A ++ + +LG ++ I H + SH LSPE + GI Sbjct: 303 GGAVVAMKVKGDRAALNRLVEALQIFVLADSLGGVESMINHSWSMSHCSLSPEQKGVMGI 362 Query: 376 GDSLIRVAVGLEDLDDLKADMARGLAAL 403 ++L+R++VG+ED DL D+ L AL Sbjct: 363 SENLLRLSVGIEDYRDLVEDLDGALKAL 390 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: 353 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: 393 Length adjustment: 31 Effective length of query: 372 Effective length of database: 362 Effective search space: 134664 Effective search space used: 134664 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