Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_013420935.1 RVAN_RS17005 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P9WGB5 (406 letters) >NCBI__GCF_000166055.1:WP_013420935.1 Length = 397 Score = 410 bits (1054), Expect = e-119 Identities = 210/392 (53%), Positives = 273/392 (69%), Gaps = 4/392 (1%) Query: 15 DGVSQATVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSRYGNPT 74 DG+ T+ V G LRS ET+EA+YL SG+ Y SAA AE F GE + YVYSRYGNPT Sbjct: 8 DGLHPDTLLVHSGTLRSPHGETSEALYLNSGFTYESAAEAEARFKGEAEGYVYSRYGNPT 67 Query: 75 VSVFEERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILP 134 V++FE R+ +EGA AA TASGMAAVF SL + L AGD ++ A+++FG+ + EILP Sbjct: 68 VTMFETRIAALEGAEAARGTASGMAAVFASLASYLRAGDHVIGAKAVFGASRAIIEEILP 127 Query: 135 RWGVQTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLD 194 R+G+++ VDG DL W A+ T+ +F E+P+NP +VDI V +AH AGA +++D Sbjct: 128 RFGIESTVVDGRDLDAWRAAIRPNTRVLFCESPANPTLDIVDIEGVAGIAHDAGAILMVD 187 Query: 195 NVFATPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAM 254 NVFATPLLQ+ G DVV+YS TKHIDGQGR LGG IL ++I+ VQ +R TGP + Sbjct: 188 NVFATPLLQRPLKFGADVVIYSATKHIDGQGRCLGGVILSTTKFIEEHVQGFLRQTGPTL 247 Query: 255 SAFNAWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQM 314 SAFNAWV+LKGLETL +RV+ +ASA +IA+FL+ + V YP HPQ LAKRQM Sbjct: 248 SAFNAWVMLKGLETLTVRVERESASAAKIADFLSEQRGIARVMYPGRADHPQAALAKRQM 307 Query: 315 SGGGTVVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEG 374 + GG +V F+LD +D F LD +R+I ISNNLGDAKSL+ HPATTTH+ + E Sbjct: 308 ASGGPLVAFSLDGDKDA----TFRFLDALRVIKISNNLGDAKSLIAHPATTTHQKLSDEA 363 Query: 375 RAAIGLGDGVVRISVGLEDTDDLIADIDRALS 406 +A +G+ G +R+SVGLE DDLI DI +AL+ Sbjct: 364 KAELGITAGTLRLSVGLEHADDLITDIAQALT 395 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: 457 Number of extensions: 15 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: 397 Length adjustment: 31 Effective length of query: 375 Effective length of database: 366 Effective search space: 137250 Effective search space used: 137250 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