Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate YP_001312755.1 Smed_4014 cystathionine gamma-synthase
Query= SwissProt::Q83A83 (387 letters) >NCBI__GCF_000017145.1:YP_001312755.1 Length = 400 Score = 268 bits (684), Expect = 3e-76 Identities = 146/379 (38%), Positives = 232/379 (61%), Gaps = 15/379 (3%) Query: 22 PDPLTGAVMTPIYTAST-------YAQKSPGVHQGYE-YSRSQNPTRFAYERCVADLESG 73 P+ + ++ PIY ++ Y Q G + YSR NPT + +E +A L G Sbjct: 17 PEEHSQSISYPIYMSANFQYDGDIYDQIVAGARKEVNIYSRCGNPTEYKFEEHIAKLTGG 76 Query: 74 QHGFAFASGMAATA-TILELLQPGDHVVVMDDVYGGSYRLFENVRKRSAGLSFSFVDFTD 132 A ASGMAA + + +L+ GDH+V Y ++ F++ R + GL S VD TD Sbjct: 77 TACLATASGMAAISHALFGILKAGDHIVADLTTYSSTHEFFDH-RAQDFGLKVSLVDCTD 135 Query: 133 ENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTFATPIIQRPLE 192 V A+T +TK+L+VE+ +NP +K+ L + E+A + I+ + DNTFA+P + RP + Sbjct: 136 VRAVENALTEETKVLYVEAIANPTMKVPPLKALVELAHARGIVVICDNTFASPAVCRPHD 195 Query: 193 LGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLKYLQ----NAIGAIAAPFDSFMV 248 G D+V SATK++ GH+D +GGV + + + L+ ++ N +GA +PF+++++ Sbjct: 196 FGVDVVVESATKFIGGHNDAVGGVITLKSDILPPDWLEDVRWNTLNKLGAPLSPFNAWLL 255 Query: 249 LRGLKTLAIRMERHCENAMQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMRYFGGMIS 308 LRG +TLA+R+E+ C NA+ LA+ LE HP+V+RV+YPGLPSHP ++ AK+Q+R G M+S Sbjct: 256 LRGAQTLALRLEKQCANALALAKHLEAHPRVRRVFYPGLPSHPNYASAKEQLRGGGAMLS 315 Query: 309 VELKCDLNETKKVLERCQLFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIR 368 ++ D ++L+R QL + A SLGG+ + + PA M IP ER+ +G+ DG +R Sbjct: 316 FQVD-DEASGVRLLKRLQLCSFAASLGGLRTTTQVPATMAFLDIPSQEREAMGVVDGLVR 374 Query: 369 LSVGIEAITDLRHDLEAAL 387 SVGIE I D+ D+++A+ Sbjct: 375 FSVGIEHIDDIIADVDSAI 393 Lambda K H 0.319 0.134 0.385 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: 385 Number of extensions: 15 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: 387 Length of database: 400 Length adjustment: 31 Effective length of query: 356 Effective length of database: 369 Effective search space: 131364 Effective search space used: 131364 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 (21.8 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