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_049755415.1 AFER_RS07735 PLP-dependent transferase
Query= SwissProt::O31632 (390 letters) >NCBI__GCF_000023265.1:WP_049755415.1 Length = 368 Score = 190 bits (482), Expect = 6e-53 Identities = 136/334 (40%), Positives = 186/334 (55%), Gaps = 19/334 (5%) Query: 49 YSRSGTPTRTALEETIAALEGGTRGFAFSSGMAAISTAFLLLSQGDHVLVTEDVYGGTFR 108 Y R PT A E I LEGGT AF SG AA T LLL+ G LV D Y GT + Sbjct: 48 YGRHTNPTWEAFEALIGELEGGT-AVAFGSGAAA--TFALLLALGPRALVVADSYMGTRQ 104 Query: 109 MVTEVLTRF-GIEHTFVDMTDRNEVARSIKPNTKVIYMETPSNPTLGITDIKAVVQLAKE 167 + + R GIE V+ +D + + P + V+ +ETPSNP L I + + E Sbjct: 105 LARWLGARIPGIE--LVEPSDLDAHLDRLAPGS-VVLIETPSNPLLVTYPIATLAKRIHE 161 Query: 168 NGCLTFLDNTFMTPALQRPLDLGVDIVLHSATKFLSGHSDVLSGLAAVKDEELGKQLYKL 227 G L +D+T TP LQRPL LG D+V+HSA+KFLSGHSDVL G+ DE+L ++ ++ Sbjct: 162 RGGLLAVDSTLATPVLQRPLTLGADVVVHSASKFLSGHSDVLGGVLVASDEDLVARVGEV 221 Query: 228 QNAFGAVLGVQDCWLVLRGLKTLQVRLEKASQTAQRLAEFFQKHPAVKRVYYPGLADHPG 287 + GA++G + +L RGL+TL VR+E+AS TA LA + V YPG D Sbjct: 222 RELTGAIIGPVEAYLCFRGLRTLAVRVERASATATTLAMRLRDRLG-DTVRYPGF-DSEL 279 Query: 288 AETHKSQSTGAGAVLSFELESKEAVKKLVENVSLPVFAVSLGAVESILSYPATMSHAAMP 347 + QS G GA+++ ELES + +++ +SL A SLG VES+ P Sbjct: 280 VGPGRQQSAG-GALVALELESAQQADAMLDGLSLFHHATSLGGVESLAE-----RRGRYP 333 Query: 348 KEEREKRGITDGLLRLSVGVEHADDLEHDFEQAL 381 E+R I +GL+RLSVG+E +DL D ++AL Sbjct: 334 GEDR----IGEGLVRLSVGLEDVEDLWGDLDRAL 363 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: 336 Number of extensions: 14 Number of successful extensions: 5 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: 368 Length adjustment: 30 Effective length of query: 360 Effective length of database: 338 Effective search space: 121680 Effective search space used: 121680 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