Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate SMc02217 SMc02217 O-succinylhomoserine sulfhydrylase
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__Smeli:SMc02217 Length = 394 Score = 254 bits (649), Expect = 3e-72 Identities = 141/385 (36%), Positives = 227/385 (58%), Gaps = 11/385 (2%) Query: 5 TLMIHGGITGDEKTGAVSVPIY--QVSTYKQPKA------GQHTGYEYSRTANPTRTALE 56 T ++HGG T + G S I+ Q Y +A G+ G+ Y+R +PT E Sbjct: 9 TQLVHGG-TLRSQYGETSEAIFLTQGFVYDSSEAAEARFKGETDGFIYARYGSPTNDMFE 67 Query: 57 ALVTELESGEAGYAFSSGMAAITAVMML-FNSGDHVVLTDDVYGGTYRVMTKVLNRLGIE 115 + LE E A +SGMAA++A ++ +GDH+V ++G V+ + + G+E Sbjct: 68 KRMCMLEGAEDARATASGMAAVSAAILCQVKAGDHIVAARALFGSCRWVVETLAPKYGVE 127 Query: 116 STFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNTFNT 175 T VD + E A+RPNTK ++E+PTNP L++ D+ +A +A + G ++VDN F T Sbjct: 128 CTLVDGRDLKNWEDAVRPNTKVFFLESPTNPTLEVIDIAGVARLADQIGAKVVVDNVFAT 187 Query: 176 PYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASKELGEELHFVQNSTGGVLGPQDS 235 P FQ+PL LGA +V++SATK++ G +GG+V++ + + E LH TG + P ++ Sbjct: 188 PLFQKPLELGAHVVVYSATKHIDGQGRCLGGVVLSDKQWVDENLHDYFRHTGPAMSPFNA 247 Query: 236 WLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYYPGSSNHPGHELAKTQGAGFGG 295 W L++GI+TL LR++ ++AR++A FL P V + YPG +HP ++ Q +G Sbjct: 248 WTLLKGIETLPLRVKQQTESARRVADFLAEQPQVARVIYPGRKDHPQADVIAKQMSGGST 307 Query: 296 MISFDI-GSEERVDAFLGNLKLFTIAESLGAVESLISVPARMTHASIPRERRLELGITDG 354 +++F++ G +E A L++ I+ +LG +SLI+ PA TH ++ E R ELGI+ G Sbjct: 308 LVAFELKGGKEAAFALQNALEIIRISNNLGDSKSLITHPATTTHKNLTDEARAELGISAG 367 Query: 355 LIRISVGIEDAEDLLEDIGQALENI 379 +R S GIED+EDL+ED +AL+ + Sbjct: 368 TVRFSAGIEDSEDLIEDFARALKGV 392 Lambda K H 0.316 0.134 0.375 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: 338 Number of extensions: 11 Number of successful extensions: 3 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: 379 Length of database: 394 Length adjustment: 30 Effective length of query: 349 Effective length of database: 364 Effective search space: 127036 Effective search space used: 127036 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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