Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate 200974 SO1812 methionine gamma-lyase (NCBI ptt file)
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__MR1:200974 Length = 397 Score = 322 bits (825), Expect = 1e-92 Identities = 173/385 (44%), Positives = 241/385 (62%), Gaps = 11/385 (2%) Query: 2 KKKTLMIHGGITGDEKTGAVSVPIYQVSTYK--------QPKAGQHTGYEYSRTANPTRT 53 K T IH G E G++ P+YQ +T+ + AG GY Y+R NPT Sbjct: 10 KAATQAIHAGHER-EAFGSLVTPLYQTATFVFDSAQQGGERFAGNEPGYIYTRLGNPTVA 68 Query: 54 ALEALVTELESGEAGYAFSSGMAAITAVMML-FNSGDHVVLTDDVYGGTYRVMTKVLNRL 112 LE + LE EA A +SGM A++A ++ GDH+V ++ VYG T+ +MT R Sbjct: 69 ELERKMAILERAEAAAATASGMGAVSAALLANLQIGDHLVASNAVYGCTFALMTNQFARF 128 Query: 113 GIESTFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNT 172 GIE T VD S E +E+AI+PNTK I+ ETP NP L++ DL+ +A IAK+ + IVDNT Sbjct: 129 GIEVTLVDFSDVELIERAIKPNTKVIFCETPVNPHLQVFDLSAIAAIAKRHSLTSIVDNT 188 Query: 173 FNTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASKELGEELHFVQNSTGGVLGP 232 F TP QQP+ LG D+V+HSATKYL GH DV+ G+V + +L + + G V+ P Sbjct: 189 FMTPLLQQPIALGIDVVVHSATKYLNGHGDVIAGIVCGSEAQLHRVKYEILKDIGAVMSP 248 Query: 233 QDSWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYYPGSSNHPGHELAKTQGAG 292 D+WL++RG+KTL +R++ ++A+++A FLE HPAV +YYPG +H GH Q Sbjct: 249 HDAWLILRGLKTLDVRLQRHCESAQRVAEFLEQHPAVTRVYYPGLKSHSGHRFIGQQMRR 308 Query: 293 FGGMISFDIGSE-ERVDAFLGNLKLFTIAESLGAVESLISVPARMTHASIPRERRLELGI 351 GG+I+F++ ++ + AF+GNLKLF+IA SLG ESLI PA MTH+ E R GI Sbjct: 309 AGGVIAFELAADFTQAMAFVGNLKLFSIAVSLGDAESLIQHPASMTHSPYSPEARAAAGI 368 Query: 352 TDGLIRISVGIEDAEDLLEDIGQAL 376 D L+RISVG+ED +D++ D+ QAL Sbjct: 369 GDNLLRISVGLEDCDDIIADLSQAL 393 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: 360 Number of extensions: 12 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: 397 Length adjustment: 30 Effective length of query: 349 Effective length of database: 367 Effective search space: 128083 Effective search space used: 128083 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