Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_029134797.1 A3GO_RS0119315 cystathionine gamma-synthase
Query= SwissProt::P9WGB5 (406 letters) >NCBI__GCF_000428045.1:WP_029134797.1 Length = 390 Score = 240 bits (613), Expect = 5e-68 Identities = 147/387 (37%), Positives = 214/387 (55%), Gaps = 8/387 (2%) Query: 20 ATVGVRGGMLRSGFEETAEAMYLTSGYVYGSAAVAEKSFAGELDHYVYSRYG-NPTVSVF 78 AT V G L +Y T+ + + A G +Y+RYG NPT+ Sbjct: 10 ATRCVHAGELADSHGSPHTPIYATTTFKFADTAALLDVVEGRQAGSLYTRYGLNPTIQAL 69 Query: 79 EERLRLIEGAPAAFATASGMAAVFTSLGALLGAGDRLVAARSLFGSCFVVCSEILPRWGV 138 E +L +EGA AAFA ASGMAA L + +V +G + +E LP G+ Sbjct: 70 EAKLASLEGAEAAFAFASGMAAEAALF--LTHGREGIVCIGDAYGGTLELIAEQLPLLGI 127 Query: 139 QTVFVDGDDLSQWERALSVPTQAVFFETPSNPMQSLVDIAAVTELAHAAGAKVVLDNVFA 198 T + G +L++ + L+ + VF ETP+NP L DIAA+ + HA GA + +DN FA Sbjct: 128 PTHLILGSELNRLDGLLAGGVRLVFLETPTNPALELFDIAALADQVHAHGALLAVDNTFA 187 Query: 199 TPLLQQGFPLGVDVVVYSGTKHIDGQGRVLGGAILGDREYIDGPVQKLMRHTGPAMSAFN 258 +P+ QQ LG DVVV+S TK++ G + GA++G + +D PV ++ G + Sbjct: 188 SPVNQQPLALGADVVVHSATKYLGGHSDLTAGALMGSKALLD-PVWGWRKNLGSMPAPET 246 Query: 259 AWVLLKGLETLAIRVQHSNASAQRIAEFLNGHPSVRWVRYPYLPSHPQYDLAKRQMSGGG 318 L + L TL +RV+ NA+AQ IAE + HP +R V YP L P ++LA RQMSG G Sbjct: 247 CGQLARSLRTLVVRVRQQNATAQAIAEAMAHHPRIRRVFYPGLTDFPGHELAVRQMSGFG 306 Query: 319 TVVTFALDCPEDVAKQRAFEVLDKMRLIDISNNLGDAKSLVTHPATTTHRAMGPEGRAAI 378 ++T +D D A A ++D+++L ++ +LG +SLVT P TTTH + + RA Sbjct: 307 GMLTIEVDA--DTAATSA--MVDRLKLFSLAASLGGVESLVTQPVTTTHHGLSEDERARR 362 Query: 379 GLGDGVVRISVGLEDTDDLIADIDRAL 405 G+ +VR+SVGLED DLIAD+ +AL Sbjct: 363 GISGAMVRLSVGLEDAGDLIADLQQAL 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: 404 Number of extensions: 19 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: 390 Length adjustment: 31 Effective length of query: 375 Effective length of database: 359 Effective search space: 134625 Effective search space used: 134625 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