Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012384038.1 BIND_RS05265 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P9WGB5 (406 letters) >NCBI__GCF_000019845.1:WP_012384038.1 Length = 408 Score = 418 bits (1074), Expect = e-121 Identities = 213/397 (53%), Positives = 277/397 (69%), Gaps = 4/397 (1%) Query: 10 PKALPDGVSQATVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSR 69 P P+G AT V GG RS F ETAEA++LT GYVY + AE F GE +VYSR Sbjct: 6 PPRDPEGWRTATRLVHGGTTRSPFGETAEAIFLTQGYVYPTMEAAEARFKGEEPGFVYSR 65 Query: 70 YGNPTVSVFEERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVC 129 Y NPT ++FEER+ L+EGA AA ATASGMAAV +L A L AGD +VA+R+LFGSC + Sbjct: 66 YNNPTNAMFEERMALLEGAEAARATASGMAAVTAALLAPLKAGDHVVASRALFGSCLYIV 125 Query: 130 SEILPRWGVQTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGA 189 E+LPR+G+ + VDG D W+ AL TQ +F E+P+NP + DIAAV +AHA GA Sbjct: 126 EELLPRYGIASTLVDGKDFKAWKDALRPQTQTLFLESPTNPSLEVYDIAAVAAIAHAHGA 185 Query: 190 KVVLDNVFATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRH 249 ++V+DN FA+P+LQ+ LG D VVYS TKHIDGQGR LGG +L +++I+ +Q +R Sbjct: 186 RLVVDNAFASPMLQKPLQLGADCVVYSATKHIDGQGRCLGGVVLSSKDFIETHLQTYLRQ 245 Query: 250 TGPAMSAFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDL 309 TGPA+S FNAW+LLK LETL +RVQ A+A ++A+FL HP + YP HPQ ++ Sbjct: 246 TGPALSPFNAWILLKSLETLPLRVQQQMANAAKVADFLADHPLIARCFYPGRADHPQAEI 305 Query: 310 AKRQMSGGGTVVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRA 369 KRQM GGGT+V F + K AF + + +I ISNNLGDAKSL+THPATTTH+ Sbjct: 306 VKRQMLGGGTMVAFEV----TGGKPAAFAFANALSIIKISNNLGDAKSLITHPATTTHQR 361 Query: 370 MGPEGRAAIGLGDGVVRISVGLEDTDDLIADIDRALS 406 + PE RA +G+G+G++R+SVGLED +DLIAD+ AL+ Sbjct: 362 LTPEARATMGIGEGLLRLSVGLEDAEDLIADLQAALA 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: 467 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: 408 Length adjustment: 31 Effective length of query: 375 Effective length of database: 377 Effective search space: 141375 Effective search space used: 141375 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