Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate CCNA_02321 CCNA_02321 O-succinylhomoserine sulfhydrylase
Query= SwissProt::P9WGB5 (406 letters) >FitnessBrowser__Caulo:CCNA_02321 Length = 394 Score = 401 bits (1031), Expect = e-116 Identities = 207/386 (53%), Positives = 272/386 (70%), Gaps = 5/386 (1%) Query: 20 ATVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSRYGNPTVSVFE 79 AT +RGG+ RS F ETAEA+YLT G+ Y SA A++ FAGE +VYSR+ NPTV +FE Sbjct: 11 ATKLIRGGIARSQFMETAEALYLTQGFTYDSAEGADRRFAGEDPGFVYSRFNNPTVKMFE 70 Query: 80 ERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQ 139 +RL L+EGA A A+GMA++ +L L+ AGD +VA R+LFGSC + SE LPR+GV+ Sbjct: 71 DRLALLEGAEVCRAQATGMASIHAALMGLVRAGDHVVAGRALFGSCRWIVSEWLPRFGVE 130 Query: 140 TVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFAT 199 T FVD D WE A+ T+AV ETPSNP+ + DI AV+ELAHA GAKV++DNVFAT Sbjct: 131 TTFVDATDPKAWEAAMRPNTKAVLVETPSNPVLEITDIRAVSELAHAVGAKVIVDNVFAT 190 Query: 200 PLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMSAFNA 259 P+ Q+ LG DVVVYS TKHIDGQGRVLGGAIL + + +RHTGP++S FNA Sbjct: 191 PIFQKPLELGADVVVYSATKHIDGQGRVLGGAILTSEAINEEFYRDSLRHTGPSLSPFNA 250 Query: 260 WVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMSGGGT 319 WV+LKGLETL +RV+ SA +A + H V+ V YP+ P HP +++AK QM+GGGT Sbjct: 251 WVMLKGLETLDLRVRRQADSAFALANTIAEHKKVQTVLYPFRPDHPGHNVAKAQMTGGGT 310 Query: 320 VVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAIG 379 V+ L +++ AF+ L+ + ++DISNNLGDAKS+ THP TTTHR++ R ++G Sbjct: 311 VIALDLG-----SREAAFKFLNALEIVDISNNLGDAKSMATHPPTTTHRSVPEAERPSLG 365 Query: 380 LGDGVVRISVGLEDTDDLIADIDRAL 405 + +G VR+SVGLE +DL D+ RAL Sbjct: 366 VTEGGVRLSVGLESVEDLKRDVIRAL 391 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: 436 Number of extensions: 18 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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