Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate 3609021 Dshi_2410 O-succinylhomoserine sulfhydrylase (RefSeq)
Query= SwissProt::P9WGB5 (406 letters) >FitnessBrowser__Dino:3609021 Length = 392 Score = 402 bits (1034), Expect = e-117 Identities = 202/384 (52%), Positives = 271/384 (70%), Gaps = 5/384 (1%) Query: 24 VRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFA-GELDHYVYSRYGNPTVSVFEERL 82 V G RS + E AEA++LT G+VY +A AE F D ++Y+RYGNPTV +FE+R+ Sbjct: 11 VHAGTRRSQYGEVAEAIFLTQGFVYDTAEAAEARFIEAGADEFIYARYGNPTVRMFEDRI 70 Query: 83 RLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTVF 142 +EG AFATASGMAAV +L ++L AGD +V+AR+LFGSC + E+L R+GV+ F Sbjct: 71 AAVEGTEDAFATASGMAAVNGALASMLRAGDHVVSARALFGSCLYILEEVLTRYGVEVTF 130 Query: 143 VDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFATPLL 202 VDG DL+ W A+ T+AVFFET SNP ++DI AV +LAHA GA V++DNVFATP+ Sbjct: 131 VDGTDLAAWRAAIRPDTKAVFFETISNPTLEVIDIEAVAKLAHAVGALVIVDNVFATPIF 190 Query: 203 QQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMSAFNAWVL 262 + G DV+VYS TKHIDGQGR LGG I G R+++ + ++HTG ++S FNAWV+ Sbjct: 191 SRAKDQGADVIVYSATKHIDGQGRCLGGVICGTRDFVRKVAEPYLKHTGGSLSPFNAWVM 250 Query: 263 LKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMSGGGTVVT 322 LK +ETL +RV+ +AQ +AE L GH ++ V +P+LPSHPQYDLA+ QM+ GGTV+ Sbjct: 251 LKSMETLDLRVRAQAETAQALAETLEGHAALEKVIFPHLPSHPQYDLARAQMAAGGTVL- 309 Query: 323 FALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAIGLGD 382 ALD K AF L+ + ++ ISNNLGDAKS+ THPATTTH+ + PE RA +G+ D Sbjct: 310 -ALDIKG--GKAGAFRFLNALEIVTISNNLGDAKSIATHPATTTHQRLTPEQRAGLGITD 366 Query: 383 GVVRISVGLEDTDDLIADIDRALS 406 G++R+SVGLED DL+ D+ AL+ Sbjct: 367 GLIRLSVGLEDAGDLLRDLQTALA 390 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: 470 Number of extensions: 19 Number of successful extensions: 3 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: 392 Length adjustment: 31 Effective length of query: 375 Effective length of database: 361 Effective search space: 135375 Effective search space used: 135375 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 09 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