Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate GFF1560 PGA1_c15810 pyridoxal phosphate-dependent enzyme, cysteine / methionine metabolism
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__Phaeo:GFF1560 Length = 385 Score = 221 bits (563), Expect = 3e-62 Identities = 130/335 (38%), Positives = 182/335 (54%), Gaps = 3/335 (0%) Query: 37 GQHTGYEYSRTANPTRTALEALVTELESGEAGYAFSSGMAAITAVMM-LFNSGDHVVLTD 95 G+ GY YSR +P + + +E G SGMAA++AV++ L +GDHV+ + Sbjct: 38 GRVHGYTYSREGHPNADVVAKRLDAMEGMPGGVVTGSGMAAVSAVLLGLLKTGDHVIGGN 97 Query: 96 DVYGGTYRVMTKVLNRLGIESTFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTL 155 +YG + R+M + L RLGIE+T + V+ AIRP T I +E +NP L + D+ Sbjct: 98 QLYGRSMRLMAEDLPRLGIETTLANPGDVAAVKAAIRPETTMILVEAVSNPTLAVADIDG 157 Query: 156 MADIAKKAGVLLIVDNTFNTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASKEL 215 +A + K +LL+VDNTF TP QP GADIV+HS TK L GHSDV+ G VV E+ Sbjct: 158 LAQLCKDRDILLVVDNTFTTPRGFQPFDHGADIVIHSITKLLAGHSDVMLGYVVAKDPEI 217 Query: 216 GEELHFVQNSTGGVLGPQDSWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYYP 275 L +TG P D WL RG+ + LR E A +A L P V+ + YP Sbjct: 218 NTRLSVYVVTTGMTPSPFDCWLAERGMLSFELRFERAQATAVTLADHLAGLPGVKRVIYP 277 Query: 276 GSSNHPGHELAKTQGAGFG-GMISFDI-GSEERVDAFLGNLKLFTIAESLGAVESLISVP 333 +HP HE A G G M+SF++ G +AF A +LG V + +S P Sbjct: 278 TRKDHPDHERAMALLDGKGCNMVSFELEGGRAAANAFTRGADGLNFAPTLGDVGTTLSHP 337 Query: 334 ARMTHASIPRERRLELGITDGLIRISVGIEDAEDL 368 A +H ++ E R +LG+++G RISVG+ED E L Sbjct: 338 ASSSHRALSTEDRAKLGLSEGFFRISVGLEDPETL 372 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: 368 Number of extensions: 15 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: 385 Length adjustment: 30 Effective length of query: 349 Effective length of database: 355 Effective search space: 123895 Effective search space used: 123895 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