Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012755917.1 RLEG_RS00965 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P9WGB5 (406 letters) >NCBI__GCF_000023185.1:WP_012755917.1 Length = 394 Score = 394 bits (1012), Expect = e-114 Identities = 198/386 (51%), Positives = 267/386 (69%), Gaps = 4/386 (1%) Query: 20 ATVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSRYGNPTVSVFE 79 AT V GG LRS + ET+EA+YLT G+VY ++ AE F GE + ++Y+RYG+PT +FE Sbjct: 8 ATQLVHGGTLRSQYGETSEAIYLTQGFVYETSEAAEARFKGETEGFIYARYGSPTNDMFE 67 Query: 80 ERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQ 139 +R+ ++EGA A ATASGMAAV ++ L +GD +VAAR+LFGSC V + P++G+ Sbjct: 68 KRMCMLEGAEDARATASGMAAVTAAILCQLKSGDHIVAARALFGSCRWVVETLAPKYGID 127 Query: 140 TVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFAT 199 +DG DL+ WE+A++ T+ F E+P+NP ++DIA V +LA+ GAKVV+DNVFAT Sbjct: 128 CTLIDGRDLANWEKAITPKTKVFFLESPTNPTLEVIDIAGVAKLANQVGAKVVVDNVFAT 187 Query: 200 PLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMSAFNA 259 PL Q+ LG +VVYS TKHIDGQGR LGG +L D+E+ID + RHTGPAMS FNA Sbjct: 188 PLFQKPLELGAHIVVYSATKHIDGQGRCLGGVVLSDKEWIDENLHDYFRHTGPAMSPFNA 247 Query: 260 WVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMSGGGT 319 W LLKG+ETL +RV+ +A +IA+FL V V YP HPQ D+ +QM+GG T Sbjct: 248 WTLLKGIETLPLRVRQQTENAAKIADFLAEQGKVAKVIYPGRKDHPQADIIAKQMTGGST 307 Query: 320 VVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAIG 379 +V F L +D AF + + + ++ ISNNLGD+KSL+THPATTTH+ + E RA +G Sbjct: 308 LVAFELKGGKDA----AFALQNALDIVKISNNLGDSKSLITHPATTTHKNLTDEARAELG 363 Query: 380 LGDGVVRISVGLEDTDDLIADIDRAL 405 + G VR+S G+EDTDDLI D +AL Sbjct: 364 ISPGTVRLSAGIEDTDDLIEDFAKAL 389 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: 440 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: 394 Length adjustment: 31 Effective length of query: 375 Effective length of database: 363 Effective search space: 136125 Effective search space used: 136125 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