Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_058930869.1 AU252_RS11760 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P9WGB5 (406 letters) >NCBI__GCF_001484605.1:WP_058930869.1 Length = 402 Score = 562 bits (1449), Expect = e-165 Identities = 280/391 (71%), Positives = 329/391 (84%), Gaps = 1/391 (0%) Query: 16 GVSQATVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSRYGNPTV 75 G S T VRGG+ R+ F+ET E ++L SG+VY SAA AE++F GE + +VYSRYGNP+V Sbjct: 9 GWSAETQAVRGGLDRTNFQETTEPVFLNSGFVYESAAAAERAFTGEDERFVYSRYGNPSV 68 Query: 76 SVFEERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPR 135 + F+ERLRL+EG A FATASGM+AVFT+LGALL AGDR+VAARSLFGSCFV+ +EILPR Sbjct: 69 ATFQERLRLLEGTEACFATASGMSAVFTALGALLAAGDRVVAARSLFGSCFVILNEILPR 128 Query: 136 WGVQTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDN 195 WGV+TVFVDG DL QW ALS PT AVFFE+PSNPMQ +VDIAAV+ELAHAAGA VV+DN Sbjct: 129 WGVETVFVDGPDLEQWAAALSEPTTAVFFESPSNPMQEIVDIAAVSELAHAAGATVVVDN 188 Query: 196 VFATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMS 255 VFATPLLQ+ LG DV+VYSGTKHIDGQGRVLGGAILG +E+IDGPV++LMRHTGPA+S Sbjct: 189 VFATPLLQRCGQLGADVIVYSGTKHIDGQGRVLGGAILGTKEFIDGPVKQLMRHTGPALS 248 Query: 256 AFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMS 315 AFNAWVL KGLET+A+RV HS+ASA R+AE+L P+V WVRYP L SHPQY+LA +QM Sbjct: 249 AFNAWVLTKGLETMALRVNHSSASALRLAEWLEQQPAVSWVRYPLLKSHPQYELAAKQMK 308 Query: 316 GGGTVVTFALDCPED-VAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEG 374 GGTV+T L K+ AF +LD +R+IDISNNLGDAKSL+THPATTTHRAMGPEG Sbjct: 309 AGGTVLTLELATTGGRSGKEAAFALLDALRIIDISNNLGDAKSLITHPATTTHRAMGPEG 368 Query: 375 RAAIGLGDGVVRISVGLEDTDDLIADIDRAL 405 RAAIGL DGVVR+SVGLED DDLI D+++AL Sbjct: 369 RAAIGLSDGVVRLSVGLEDVDDLIGDLEQAL 399 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: 570 Number of extensions: 22 Number of successful extensions: 2 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: 402 Length adjustment: 31 Effective length of query: 375 Effective length of database: 371 Effective search space: 139125 Effective search space used: 139125 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 10 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