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 WP_012471102.1 GLOV_RS15175 cystathionine gamma-synthase
Query= SwissProt::O31632 (390 letters) >NCBI__GCF_000020385.1:WP_012471102.1 Length = 377 Score = 424 bits (1089), Expect = e-123 Identities = 202/375 (53%), Positives = 275/375 (73%) Query: 8 LETQLVHNPFKTDGGTGAVSVPIQHASTFHQSSFEEFGAYDYSRSGTPTRTALEETIAAL 67 + TQL+H D TGA+ VP+ ST+ Q+SFE FG YDY+R PTR A+EE +A L Sbjct: 3 IATQLIHAGPTVDQQTGALGVPVYQISTYRQTSFEHFGKYDYARGDNPTREAVEEVVARL 62 Query: 68 EGGTRGFAFSSGMAAISTAFLLLSQGDHVLVTEDVYGGTFRMVTEVLTRFGIEHTFVDMT 127 EGGTR AF+SGMAAIST ++ S GDH++V +DVYGG +R++T + +R GI +FVD T Sbjct: 63 EGGTRCLAFASGMAAISTTLMIFSPGDHLVVCDDVYGGAYRVLTSIFSRMGINASFVDAT 122 Query: 128 DRNEVARSIKPNTKVIYMETPSNPTLGITDIKAVVQLAKENGCLTFLDNTFMTPALQRPL 187 D + +I+P T+ +Y+ETPSNP L +TD++ +AK +G +T +DNTFMTP LQRPL Sbjct: 123 DLAAIEAAIRPETRALYLETPSNPLLKVTDLRGAAAIAKRHGIITLVDNTFMTPYLQRPL 182 Query: 188 DLGVDIVLHSATKFLSGHSDVLSGLAAVKDEELGKQLYKLQNAFGAVLGVQDCWLVLRGL 247 +LG DIVLHS TKFL+GHSDV+ G A +D+ELG+++ +QNAFG LG QD +L LRG+ Sbjct: 183 ELGCDIVLHSGTKFLNGHSDVICGFAVTRDDELGQRIRYIQNAFGTGLGPQDSFLTLRGI 242 Query: 248 KTLQVRLEKASQTAQRLAEFFQKHPAVKRVYYPGLADHPGAETHKSQSTGAGAVLSFELE 307 KTL+VR++++ Q + E ++HP V V+YPGL +HPG H +Q+ G GAV SFE++ Sbjct: 243 KTLKVRMDQSQQNTGIIVERLKQHPRVTAVHYPGLVEHPGHAVHAAQAEGPGAVFSFEVD 302 Query: 308 SKEAVKKLVENVSLPVFAVSLGAVESILSYPATMSHAAMPKEEREKRGITDGLLRLSVGV 367 S E ++L+EN L FAVSLG VESI+SYPA MSHA++P+EER ++GI+D L+RLSVG+ Sbjct: 303 SLETTQRLLENAHLAAFAVSLGGVESIISYPARMSHASVPREERLRKGISDTLIRLSVGL 362 Query: 368 EHADDLEHDFEQALK 382 E DDL D EQA++ Sbjct: 363 EDPDDLYADLEQAMQ 377 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: 422 Number of extensions: 9 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 360 Effective length of database: 347 Effective search space: 124920 Effective search space used: 124920 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 10 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