Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_011765155.1 AZO_RS07195 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::Q83A83 (387 letters) >NCBI__GCF_000061505.1:WP_011765155.1 Length = 434 Score = 228 bits (580), Expect = 3e-64 Identities = 147/417 (35%), Positives = 218/417 (52%), Gaps = 42/417 (10%) Query: 12 DTRVIHAGQKPDPLTGAVMTPIYTASTY----AQKSPGVHQ----GYEYSRSQNPTRFAY 63 +T +HAGQ PDP+ G+ TPI+ ++Y A ++ + G+ YSR NPT Sbjct: 10 ETLALHAGQSPDPVHGSRATPIHFTTSYVFSDADQAAALFNLERPGHVYSRISNPTTAVL 69 Query: 64 ERCVADLESGQHGFAFASGMAAT-ATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSAG 122 E VA LE G A ASG AA I L+ G H+V +YGGS+ L R G Sbjct: 70 EERVAALEGGVGAIAVASGQAALHLAITTLMGAGGHIVASRALYGGSHNLLGYTLPRF-G 128 Query: 123 LSFSFVDFTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTF 182 + +FVD D + R A+ +T++ + ES NP L ++D+ ++ +A + + + D T Sbjct: 129 IHTTFVDPHDLDAWRAAIRPETRLFFGESVGNPGLDVLDIPAVSALAHQHRLPLLVDATL 188 Query: 183 ATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAVVGDN---------KTLAEQ----- 228 +P++QRPL+LG D+V HSATKYL GH +GGV V G TL E Sbjct: 189 VSPLLQRPLDLGADLVMHSATKYLGGHGVAVGGVIVDGGRFDWEASGLFPTLTEPYDGFH 248 Query: 229 ----------LKYLQNA-------IGAIAAPFDSFMVLRGLKTLAIRMERHCENAMQLAQ 271 +L A GA +P ++F +L+GL+TL +RM H NA +A+ Sbjct: 249 GMDFAEESPVAAFLLRARREGLRDFGACLSPMNAFQILQGLETLPLRMRAHVANARAVAE 308 Query: 272 WLEKHPKVKRVYYPGLPSHPQHSIAKKQMRY-FGGMISVELKCDLNETKKVLERCQLFTL 330 L HP V++V YPGLP H H++A + + + G ++S +LK + + +LF+ Sbjct: 309 HLAAHPLVEKVAYPGLPGHRDHALAARLLPHGCGAVMSFDLKGGREGGRAFIGALRLFSH 368 Query: 331 AESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVGIEAITDLRHDLEAAL 387 ++G +SL+ HPA TH + A+ GI +G +RLSVGIE DL DL+ L Sbjct: 369 LANVGDAKSLVIHPASTTHFRMSAADLAAAGIGEGTVRLSVGIENTADLIADLDRGL 425 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: 417 Number of extensions: 22 Number of successful extensions: 6 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: 434 Length adjustment: 31 Effective length of query: 356 Effective length of database: 403 Effective search space: 143468 Effective search space used: 143468 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