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 7025489 Shewana3_2643 methionine gamma-lyase (RefSeq)
Query= SwissProt::O31632 (390 letters) >FitnessBrowser__ANA3:7025489 Length = 397 Score = 317 bits (813), Expect = 3e-91 Identities = 171/394 (43%), Positives = 238/394 (60%), Gaps = 11/394 (2%) Query: 2 SKHNWTLETQLVHNPFKTDGGTGAVSVPIQHASTFHQSSFEEFG--------AYDYSRSG 53 S W TQ +H + + G + P+ +TF S ++ G Y Y+R G Sbjct: 5 SSKQWKAATQAIHAGHEREA-FGTLVTPLYQTATFVFESAQQGGERFAGNEPGYIYTRLG 63 Query: 54 TPTRTALEETIAALEGGTRGFAFSSGMAAISTAFLL-LSQGDHVLVTEDVYGGTFRMVTE 112 PT LE +A LEG A +SGM A+S A L L GDH++ + VYG TF ++T Sbjct: 64 NPTVAELERKMAILEGAEAAAATASGMGAVSAALLANLQMGDHLVASNAVYGCTFALMTS 123 Query: 113 VLTRFGIEHTFVDMTDRNEVARSIKPNTKVIYMETPSNPTLGITDIKAVVQLAKENGCLT 172 RFGIE T VD TD + R+IKPNT+VI+ ETP NP L + D+K + +AK + ++ Sbjct: 124 QFARFGIEVTLVDFTDLAAIERAIKPNTRVIFCETPVNPHLQVFDLKGIADIAKRHQLVS 183 Query: 173 FLDNTFMTPALQRPLDLGVDIVLHSATKFLSGHSDVLSGLAAVKDEELGKQLYKLQNAFG 232 +DNTFMTP LQ+PL G+D+V+HSATK+L+GH DV++G+ +E+L + Y++ G Sbjct: 184 IVDNTFMTPLLQQPLAFGIDLVVHSATKYLNGHGDVIAGVVCGSEEQLHRVKYEILKDIG 243 Query: 233 AVLGVQDCWLVLRGLKTLQVRLEKASQTAQRLAEFFQKHPAVKRVYYPGLADHPGAETHK 292 AV+ D WL+LRGLKTL VRL++ +AQR+AEF ++HPAV RVYYPGL H G Sbjct: 244 AVMSPHDAWLILRGLKTLDVRLQRHCDSAQRVAEFLEQHPAVTRVYYPGLKSHSGHRFIG 303 Query: 293 SQSTGAGAVLSFEL-ESKEAVKKLVENVSLPVFAVSLGAVESILSYPATMSHAAMPKEER 351 Q AG V++FEL S E V + L AVSLG ES++ +PA+M+H+ E R Sbjct: 304 GQMAKAGGVIAFELAASLEQAMAFVGYLKLFSIAVSLGDAESLIQHPASMTHSPYTPEAR 363 Query: 352 EKRGITDGLLRLSVGVEHADDLEHDFEQALKEIA 385 + GI+D LLR+S+G+E D+ D QAL +A Sbjct: 364 QAAGISDNLLRISIGLEDCGDIIEDLNQALAMLA 397 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: 389 Number of extensions: 16 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: 397 Length adjustment: 31 Effective length of query: 359 Effective length of database: 366 Effective search space: 131394 Effective search space used: 131394 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