Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate NP_347030.1 CA_C0390 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_000008765.1:NP_347030.1 Length = 384 Score = 387 bits (994), Expect = e-112 Identities = 195/376 (51%), Positives = 264/376 (70%), Gaps = 16/376 (4%) Query: 3 QHVETKLAQIGNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIA 62 ++ ETK + + TG +S PIY S+ +RH G+ + TG+DY RT NPTR VE +A Sbjct: 7 RNFETKAVHGESGFESRTGAISYPIYQSSTFRHEGLNKGTGYDYSRTGNPTRDEVEKTVA 66 Query: 63 NLENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDD 122 LENG LA+SSGMAAI +++ +FK GD +IVS DLYGGTYR+FE ++ YG+ Y D Sbjct: 67 ALENGRACLAYSSGMAAISSVLTIFKGGDHIIVSDDLYGGTYRIFEEIYEHYGIEVTYTD 126 Query: 123 FSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQR 182 + + + ++ NTKA+++ETPTNPLM+ DI ++++ KEH LLIVDNTF TP Q+ Sbjct: 127 TTSTENIEKELRENTKAIYLETPTNPLMKITDIREVSKLAKEHNTLLIVDNTFMTPYYQK 186 Query: 183 PLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMR 242 PLELGADIV+HS TKYL GHND LAG V++ DERL E++ QN++GAVL PFDSWL++R Sbjct: 187 PLELGADIVLHSGTKYLCGHNDALAGFVILNDERLIEKLRFIQNSVGAVLAPFDSWLILR 246 Query: 243 GMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFR 286 G+KTL +R+ + Q NA ++A FL++ ++I+ VLYPG G M+SF Sbjct: 247 GIKTLHIRLDRQQENAIKIANFLKKHKKITKVLYPGLEEHVGHDILKSEASGFGAMISFY 306 Query: 287 LQKEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSV 346 + +E V L+++K I FAESLGGVES ITYP TQTH DIP++IR GV ++LLRFSV Sbjct: 307 VDSKETVEKVLESVKVIIFAESLGGVESLITYPYTQTHADIPDDIRKRLGVTDKLLRFSV 366 Query: 347 GIEHAEDLKEDLKQAL 362 GIE+ +DL +DL +AL Sbjct: 367 GIENVDDLIKDLDKAL 382 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: 416 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: 384 Length adjustment: 30 Effective length of query: 343 Effective length of database: 354 Effective search space: 121422 Effective search space used: 121422 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