Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_014449573.1 LFE_RS07250 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q5SHW0 (354 letters) >NCBI__GCF_000284315.1:WP_014449573.1 Length = 401 Score = 132 bits (332), Expect = 2e-35 Identities = 110/366 (30%), Positives = 173/366 (47%), Gaps = 35/366 (9%) Query: 18 DVLPLWVADMDFPPAEAIQQA-LAERARGFLGYPPREGDRELRELILEALGLEAELAFMP 76 DV + DF E I+ A +A GF Y G EL+ I+E + + + P Sbjct: 35 DVRDFTGGEPDFDTPEPIKDAAIAALKSGFTKYTAVGGIPELKSAIIEKFERDQGIVYKP 94 Query: 77 GVVV-------GLYAAVAAFTAPGQGVLTQVPIYPPFLAAIRDQRRTVLANPLRETPEGY 129 +V L+ A PG VL P + + I V+ P + +G+ Sbjct: 95 SEIVVSSGAKHSLFQIFQALVNPGDHVLLPTPAWVSYPDQILLNGGVVIGVPCLPS-DGF 153 Query: 130 RL-DLAGLERLAFATRLLLFCHPHNPTGRVFGEEELAALAQIARRHDLIVVSDELHAPLT 188 RL A LE + +R+L+ P+NP+G + +E+L +A+I ++H+LIV+SDE++ + Sbjct: 154 RLRPQALLEAITPRSRVLVLNSPNNPSGAIIPKEDLLRIAEIVKKHNLIVISDEIYEKIV 213 Query: 189 YEKPHV-PLARFLPE---RTLTLVGPGKTYNLAGLPIGAVLGPKPLVEAVKRHLPHVF-- 242 ++ +A +PE RT+ + G KTY + G IG GP P++EAV+ Sbjct: 214 FDGQETSSIASLVPEIRDRTVIVNGVSKTYAMTGWRIGYAAGPAPIIEAVETIQSQTASN 273 Query: 243 PNVLAMAAWKAALKEGGPWLKATLEQLRANRDRVAAWAKA-RGLGHHPPEGTYLAW---- 297 P +A A A++ G + K L + R + A G+ PP+G + A+ Sbjct: 274 PTSIAQKAAVVAIRSGEIYFKPMLAEYTRRRAMLLESLNAIDGIRMSPPDGAFYAFPDVS 333 Query: 298 -----------IQTPFPKAAAYFLERARVALNPGESFGRGYDTYVRLNFATYPEVLEEAL 346 I+T + +FL ARVAL PG +FG D ++R++FAT PE LEE + Sbjct: 334 GLLGKRFGDMEIRT-VTDLSEFFLAEARVALVPGSAFGS--DHHMRMSFATSPENLEEGV 390 Query: 347 RRLDGA 352 RRL A Sbjct: 391 RRLKEA 396 Lambda K H 0.322 0.140 0.433 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: 355 Number of extensions: 14 Number of successful extensions: 4 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: 354 Length of database: 401 Length adjustment: 30 Effective length of query: 324 Effective length of database: 371 Effective search space: 120204 Effective search space used: 120204 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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