Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_052665209.1 NITAL_RS05960 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P9WGB5 (406 letters) >NCBI__GCF_000969705.1:WP_052665209.1 Length = 399 Score = 512 bits (1318), Expect = e-150 Identities = 267/408 (65%), Positives = 317/408 (77%), Gaps = 12/408 (2%) Query: 1 MTDESSVRTPKA--LPDGVSQATVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSF 58 MTDE + P A LPD TV VR G RS F ET+EA++ TSGYVY +AA A +F Sbjct: 1 MTDEP-IPDPSADWLPD-----TVAVRAGTERSAFGETSEALFATSGYVYETAAEAAAAF 54 Query: 59 AGELDHYVYSRYGNPTVSVFEERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAA 118 AGE D Y+YSR GNPTVS+FEERLR +EGA A+ATASGMAAVF +L A L AGDR+VAA Sbjct: 55 AGESDRYIYSRLGNPTVSMFEERLRRLEGAEGAWATASGMAAVFNALAATLRAGDRVVAA 114 Query: 119 RSLFGSCFVVCSEILPRWGVQTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIA 178 R LFGSCF + EILPRW V+T FVDG DL QWERAL+ P QAVFFETPSNPMQ LVDIA Sbjct: 115 RGLFGSCFQILDEILPRWDVRTDFVDGSDLGQWERALATPAQAVFFETPSNPMQELVDIA 174 Query: 179 AVTELAHAAGAKVVLDNVFATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREY 238 AV+ELAHAAGA+V++DNVFATP+LQ+ LG DVVVYS TKH+DG GR +GGAILG E+ Sbjct: 175 AVSELAHAAGARVIVDNVFATPVLQRPLELGADVVVYSTTKHLDGHGRTMGGAILGTTEF 234 Query: 239 IDGPVQKLMRHTGPAMSAFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRY 298 + ++ LMRHTGP M+ FNAWV+LK LETLA+RV+ ASA +A +L HP+V VRY Sbjct: 235 LQEELRPLMRHTGPVMAPFNAWVVLKSLETLALRVERQTASALALAAWLEQHPAVEEVRY 294 Query: 299 PYLPSHPQYDLAKRQMSGGGTVVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSL 358 P L SHPQ++LA RQM+GGG++VTF + +RAFEV+D++ LIDISNNLGDAKSL Sbjct: 295 PMLASHPQHELAVRQMTGGGSIVTFWV----PGGTERAFEVIDRLALIDISNNLGDAKSL 350 Query: 359 VTHPATTTHRAMGPEGRAAIGLGDGVVRISVGLEDTDDLIADIDRALS 406 VTHPATTTH +GPE RA +G+ DGV+RISVGLED DL AD+D+ALS Sbjct: 351 VTHPATTTHHRIGPEVRAEMGVTDGVIRISVGLEDPTDLQADLDQALS 398 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: 529 Number of extensions: 17 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: 399 Length adjustment: 31 Effective length of query: 375 Effective length of database: 368 Effective search space: 138000 Effective search space used: 138000 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