Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Ga0059261_1458 Ga0059261_1458 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::P9WGB5 (406 letters) >FitnessBrowser__Korea:Ga0059261_1458 Length = 440 Score = 192 bits (487), Expect = 2e-53 Identities = 128/386 (33%), Positives = 207/386 (53%), Gaps = 26/386 (6%) Query: 40 MYLTSGYVYGSAAVAEKSFAGEL-------DHYVYSRYGNPTVSVFEERLRLIEGAPAAF 92 ++ TS +V+ +AA ++ F G + VYSR+ P + E+RL + E A A Sbjct: 58 IFATSTFVFPNAAAGKRHFEGVTGKRPGGAEGLVYSRFNGPNQEILEDRLGIWEEAEDAL 117 Query: 93 ATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGVQTV-FVDGDDLSQW 151 A +SGM+A+ T A++ GD +V + L+ + + + IL ++GV + F G + Sbjct: 118 AFSSGMSAIATLFLAMVKPGDTIVHSGPLYAATETLIARILGKFGVHWLDFPAGATREEI 177 Query: 152 ERALSVPTQA----VFFETPSNPMQSLVDIAAVTELAHA--AGAK---VVLDNVFATPLL 202 + LS ++ E+P+NP +LVD+ AV A GA + +DN F PL Sbjct: 178 DAVLSKAASGNVALIYLESPANPTNALVDVEAVAASRDAIFTGASKPPIAIDNTFLGPLW 237 Query: 203 QQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHT-GPAMSAFNAWV 261 + G D+VVYS TK+ G ++ G +LG +E I+ +LMR+T G AW+ Sbjct: 238 AKPLQQGADLVVYSLTKYAGGHSDLVAGGVLGSKELIN--TIRLMRNTIGTICDPNTAWM 295 Query: 262 LLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRY-PYLPSHP-QYDLAKRQMSGGGT 319 LL+ LETL +R+ + +A ++ E+L HP V V Y +LP Q D+ R +G G+ Sbjct: 296 LLRSLETLELRMSRAGENAIKVCEYLRTHPKVESVGYLGFLPEGSRQRDIYDRHCTGAGS 355 Query: 320 VVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAIG 379 + L E + AF LD +++ ++ +LG ++L + PA TH ++ + A+G Sbjct: 356 TFSLYLKGGE----KEAFAFLDSLKIAKLAVSLGGTETLASAPAAMTHLSVPDARKKALG 411 Query: 380 LGDGVVRISVGLEDTDDLIADIDRAL 405 + D +VRIS+G+ED DDLIAD + AL Sbjct: 412 ITDNLVRISIGVEDADDLIADFEEAL 437 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: 415 Number of extensions: 24 Number of successful extensions: 5 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: 440 Length adjustment: 32 Effective length of query: 374 Effective length of database: 408 Effective search space: 152592 Effective search space used: 152592 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