Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_012465631.1 CLIM_RS03365 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000020465.1:WP_012465631.1 Length = 381 Score = 283 bits (725), Expect = 4e-81 Identities = 154/374 (41%), Positives = 218/374 (58%), Gaps = 17/374 (4%) Query: 6 ETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLE 65 ET G D TG+V+ P++ ++ + + F Y R NPTRQ +E +A LE Sbjct: 4 ETLAIHDGQTPDPQTGSVTVPVFQTSTFEREDLSHRREFFYSRIGNPTRQALESTLALLE 63 Query: 66 NGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFSD 125 NG GLAF+SG AA + + + GD ++ + D+YGGTYR+FE + +G+ Y D Sbjct: 64 NGRFGLAFASGAAATMAALQVLRPGDHIVSALDIYGGTYRIFEQLLRPWGIGISYADNEA 123 Query: 126 EDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLE 185 + + I P TK +++E+P+NPL++ +DI IA + +E G+L+ VDNTF +P QRPLE Sbjct: 124 VESYAACIVPETKLIWLESPSNPLLRLSDIREIASLARERGILVAVDNTFASPYFQRPLE 183 Query: 186 LGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRGMK 245 LGADI +HS TKYLGGH+D++ G VV+ D L + +Q A GA+ P+D WL+MRG+K Sbjct: 184 LGADIAVHSTTKYLGGHSDVIGGAVVLNDPALLTTIKNYQAAAGAIPGPWDCWLIMRGIK 243 Query: 246 TLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRLQK 289 TL +RM++H+ANA LA LE + V YPG GML+F L+ Sbjct: 244 TLKIRMKEHEANALHLAQLLEGHPAVERVWYPGLPSHPQHELAKRQMSGFSGMLTFALKG 303 Query: 290 E-EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGI 348 V L LK A+SLGGVES + PA T + + R G + L+R SVG+ Sbjct: 304 GLPAVELLLAKLKLFALADSLGGVESLVASPAKMTLGALSAKERTKRGCSDNLVRMSVGL 363 Query: 349 EHAEDLKEDLKQAL 362 E+A DL+ DL AL Sbjct: 364 EYAGDLEADLLTAL 377 Lambda K H 0.319 0.135 0.392 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: 322 Number of extensions: 16 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: 373 Length of database: 381 Length adjustment: 30 Effective length of query: 343 Effective length of database: 351 Effective search space: 120393 Effective search space used: 120393 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 (21.7 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