Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate PP_0659 PP_0659 Cystathionine gamma-synthase
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__Putida:PP_0659 Length = 423 Score = 278 bits (711), Expect = 2e-79 Identities = 157/357 (43%), Positives = 217/357 (60%), Gaps = 11/357 (3%) Query: 26 YQVSTYKQPKAGQHTGYEYSRTANPTRTALEALVTELESGEAGYAFSSGMAAITAVMMLF 85 Y V+ KQP G+ YSR +NPT LEA + ELE E+ AFSSGMAAI+AV+ F Sbjct: 52 YDVAQGKQP------GFIYSRMSNPTVATLEAKLAELEQAESAVAFSSGMAAISAVLHTF 105 Query: 86 -NSGDHVVLTDDVYGGTYRVMTKVLNRLGIESTFVDTSSREEVEKAIRPNTKAIYIETPT 144 ++G VV T D YGGT ++ + L R+G++ DT E +E+ I +Y+ETPT Sbjct: 106 LSNGKRVVSTRDSYGGTNKIFEEFLPRMGVQVCLCDTLDTEALEREIAAGCDLLYLETPT 165 Query: 145 NPLLKITDLTLMADIAKKAGVLLIVDNTFNTPYFQQPLTLGADIVLHSATKYLGGHSDVV 204 NP LK+ D+ ++ A K G L++ DNTF TP Q PL LG D+V+HSATK+L GH DV+ Sbjct: 166 NPTLKVLDIRRLSAAAHKVGALVVADNTFATPLNQNPLALGVDVVVHSATKFLSGHGDVL 225 Query: 205 GGLVVTASKELGEELHFVQNSTGGVLGPQDSWLLMRGIKTLGLRMEAIDQNARKIASFLE 264 GG+V A + + H+ + G L P ++L++RGIKTL +R+ +A +A +L Sbjct: 226 GGVVCGAEALMAQVRHY-REINGAALDPFSAYLIIRGIKTLAVRLRQQQASAMALAHYLS 284 Query: 265 NHPAVQTLYYPGSSNHPGHELAKTQGAGFGGMISFDI-GSEERVDAFLGNLKLFTIAESL 323 P V+ + YPG H GH +AK Q GFG ++SF + G V L LK A +L Sbjct: 285 TEPLVEAVNYPGLPAHAGHAIAKAQMRGFGAIVSFVLKGGMPTVARLLPRLKYAHRAGNL 344 Query: 324 GAVESLISVPARMT-HASIPRERRLELGITDGLIRISVGIEDAEDLLEDIGQALENI 379 GAVE++ PAR T H E RL LGI++GL+RISVGIE+ +DLL D+ QA ++ Sbjct: 345 GAVETIYG-PARTTSHVENTLEERLALGISEGLVRISVGIEETDDLLADLAQACASV 400 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: 388 Number of extensions: 17 Number of successful extensions: 4 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: 423 Length adjustment: 31 Effective length of query: 348 Effective length of database: 392 Effective search space: 136416 Effective search space used: 136416 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