Align Cystathionine beta-lyase MetC; CBL; Beta-cystathionase MetC; Cysteine lyase MetC; Cysteine-S-conjugate beta-lyase MetC; EC 4.4.1.13 (characterized)
to candidate GFF1560 PGA1_c15810 pyridoxal phosphate-dependent enzyme, cysteine / methionine metabolism
Query= SwissProt::O31632 (390 letters) >FitnessBrowser__Phaeo:GFF1560 Length = 385 Score = 231 bits (589), Expect = 3e-65 Identities = 136/338 (40%), Positives = 185/338 (54%), Gaps = 3/338 (0%) Query: 47 YDYSRSGTPTRTALEETIAALEGGTRGFAFSSGMAAISTAFL-LLSQGDHVLVTEDVYGG 105 Y YSR G P + + + A+EG G SGMAA+S L LL GDHV+ +YG Sbjct: 43 YTYSREGHPNADVVAKRLDAMEGMPGGVVTGSGMAAVSAVLLGLLKTGDHVIGGNQLYGR 102 Query: 106 TFRMVTEVLTRFGIEHTFVDMTDRNEVARSIKPNTKVIYMETPSNPTLGITDIKAVVQLA 165 + R++ E L R GIE T + D V +I+P T +I +E SNPTL + DI + QL Sbjct: 103 SMRLMAEDLPRLGIETTLANPGDVAAVKAAIRPETTMILVEAVSNPTLAVADIDGLAQLC 162 Query: 166 KENGCLTFLDNTFMTPALQRPLDLGVDIVLHSATKFLSGHSDVLSGLAAVKDEELGKQLY 225 K+ L +DNTF TP +P D G DIV+HS TK L+GHSDV+ G KD E+ +L Sbjct: 163 KDRDILLVVDNTFTTPRGFQPFDHGADIVIHSITKLLAGHSDVMLGYVVAKDPEINTRLS 222 Query: 226 KLQNAFGAVLGVQDCWLVLRGLKTLQVRLEKASQTAQRLAEFFQKHPAVKRVYYPGLADH 285 G DCWL RG+ + ++R E+A TA LA+ P VKRV YP DH Sbjct: 223 VYVVTTGMTPSPFDCWLAERGMLSFELRFERAQATAVTLADHLAGLPGVKRVIYPTRKDH 282 Query: 286 PGAETHKSQSTGAGA-VLSFELE-SKEAVKKLVENVSLPVFAVSLGAVESILSYPATMSH 343 P E + G G ++SFELE + A FA +LG V + LS+PA+ SH Sbjct: 283 PDHERAMALLDGKGCNMVSFELEGGRAAANAFTRGADGLNFAPTLGDVGTTLSHPASSSH 342 Query: 344 AAMPKEEREKRGITDGLLRLSVGVEHADDLEHDFEQAL 381 A+ E+R K G+++G R+SVG+E + L F +A+ Sbjct: 343 RALSTEDRAKLGLSEGFFRISVGLEDPETLCAVFTEAV 380 Lambda K H 0.317 0.132 0.374 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: 406 Number of extensions: 21 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: 390 Length of database: 385 Length adjustment: 30 Effective length of query: 360 Effective length of database: 355 Effective search space: 127800 Effective search space used: 127800 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 (21.7 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