Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_043745532.1 AMB_RS21365 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P9WGB5 (406 letters) >NCBI__GCF_000009985.1:WP_043745532.1 Length = 403 Score = 436 bits (1122), Expect = e-127 Identities = 227/390 (58%), Positives = 286/390 (73%), Gaps = 9/390 (2%) Query: 21 TVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSRYGNPTVSVFEE 80 T VRGG+ R+ F ET+EA+++ SGYVY SA AE SF G LD VYSR+ NPTV+VFE+ Sbjct: 16 TRAVRGGLSRTNFCETSEAVFMNSGYVYDSAEEAEASFDGTLDRMVYSRFKNPTVAVFEQ 75 Query: 81 RLRLIEGAP-----AAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPR 135 RL +EGAP AA ATASGMAAV +L L AGDR+VA+ +LFGSC + +E+LPR Sbjct: 76 RLAEMEGAPPGMAVAARATASGMAAVHAALLCQLRAGDRVVASTALFGSCHWIINELLPR 135 Query: 136 WGVQTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDN 195 +GV+ VFVDG DL WE ALS PT VF ETPSNP ++D+AAV ELAH AGAKVV+DN Sbjct: 136 YGVERVFVDGTDLKSWEAALSRPTACVFLETPSNPTLEIIDLAAVCELAHKAGAKVVVDN 195 Query: 196 VFATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMS 255 VFATP+LQ LG D+VVYS TKH+DGQGR LGGA+LG E+ + +R+TGPA+S Sbjct: 196 VFATPILQSPLELGADIVVYSATKHMDGQGRCLGGAVLGSPEFCADILGPFLRNTGPALS 255 Query: 256 AFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMS 315 FNAWVLLKGLETL +R++ A+A ++A FL P V V YP L SHPQ+DLAKRQM Sbjct: 256 PFNAWVLLKGLETLDLRMERHCANALKVARFLEARPEVARVLYPGLESHPQHDLAKRQMR 315 Query: 316 GGGTVVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGR 375 G G++V L K A+++L+ + LIDISNNLGDAKSL+THP TTTH+ + PE + Sbjct: 316 GWGSIVALEL----KGGKPAAYKLLNGVELIDISNNLGDAKSLITHPWTTTHQRLSPEDK 371 Query: 376 AAIGLGDGVVRISVGLEDTDDLIADIDRAL 405 ++G+ +G++R+SVGLED DDL+ D+ RAL Sbjct: 372 LSMGITEGLLRLSVGLEDGDDLVEDLGRAL 401 Lambda K H 0.319 0.135 0.395 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: 502 Number of extensions: 18 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: 406 Length of database: 403 Length adjustment: 31 Effective length of query: 375 Effective length of database: 372 Effective search space: 139500 Effective search space used: 139500 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