Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 3607593 Dshi_1002 Cystathionine gamma-synthase (RefSeq)
Query= SwissProt::P55218 (403 letters) >FitnessBrowser__Dino:3607593 Length = 380 Score = 208 bits (530), Expect = 2e-58 Identities = 131/342 (38%), Positives = 188/342 (54%), Gaps = 14/342 (4%) Query: 63 PGNVYSRYTNPTVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVF 122 P N+YSR + +R E +AALEG A+A SGM+A A+ +L +G V++ ++ Sbjct: 48 PDNIYSRDDSEALRAVETLLAALEGGAGALAFPSGMAATAAVFRTL-PAGARVVLQSGIY 106 Query: 123 GSTISLFDKYFKRFGIQVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAE 182 T + R G+ + +D A +AC T L FVE+PSNP + VDI A A Sbjct: 107 WGTTKWVRDFCARRGVTLVEVDAADAHALGSACAAPTALVFVETPSNPWLKTVDIRAAAA 166 Query: 183 IAHAKGALLAVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGG--VVAGRG-EQM 239 AH GALL VD+ TP L +PL LGAD+V+HSATK ++G + G V A G E Sbjct: 167 AAHGAGALLVVDSTAATPVLTRPLGLGADLVMHSATKGLNGHSDVLAGALVTADAGHETW 226 Query: 240 KEVVGFLRTAGPTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAG 299 + AG L PF AWL L+G+ TL +R+ SA+AL LA+ L + V+Y G Sbjct: 227 ARIATDRHDAGAVLGPFEAWLLLRGMRTLPLRVARMSATALELAQRLSTDTRVADVFYPG 286 Query: 300 LPSHPQHELARRQQS-GFGAVVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPA 358 LP H H++A Q + GFG ++SF V G R A + + T+LG ++ + H A Sbjct: 287 LPGHAGHDIAVAQMTGGFGGLMSFLVHGDRQTALEVVGRLELFQRATSLGGVESLVEHRA 346 Query: 359 TTSHGRLSPEDRARAGIGDSLIRVAVGLEDLDDLKADMARGL 400 T + P+ +GI ++L+R++VG+ED DL AD+ R L Sbjct: 347 T-----IEPD----SGIPETLVRLSVGIEDAGDLWADLDRAL 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: 368 Number of extensions: 19 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: 380 Length adjustment: 31 Effective length of query: 372 Effective length of database: 349 Effective search space: 129828 Effective search space used: 129828 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