Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_083769343.1 AFER_RS07435 hypothetical protein
Query= SwissProt::Q5SHW0 (354 letters) >NCBI__GCF_000023265.1:WP_083769343.1 Length = 329 Score = 139 bits (351), Expect = 8e-38 Identities = 95/261 (36%), Positives = 140/261 (53%), Gaps = 14/261 (5%) Query: 104 PPFLAAIRDQRRTVLANPLRETPEGYRLDLAGLER--LAFATRLLLFCHPHNPTGRVFGE 161 PPFL+ R V+ PLRE + YRLD LER +A + L+ C+PHNPTGRV Sbjct: 66 PPFLSTPVSLGRRVVTVPLREEDD-YRLDPERLERTLIASGAKALILCNPHNPTGRVATR 124 Query: 162 EELAALAQIARRHDLIVVSDELHAPL----TYEKPHVPLARFLPERTLTLVGPGKTYNLA 217 EEL A+A + RH ++V++DE+H + P + L ER++ L KT+N+A Sbjct: 125 EELTAIADVVERHHVVVIADEIHQDIVRTGVRHVPWLSLDHAATERSVGLSAATKTFNIA 184 Query: 218 GLPIGAVLGPKPLVEAVKRHLPHVF---PNVLAMAAWKAALKEGGPWLKATLEQLRANRD 274 GL V V + + F P L + A A ++GG WL++TL++++ N + Sbjct: 185 GLKAAHVEAGSTRVAQMLGEVDAHFRSSPTSLGLLAAAVAWEQGGEWLESTLDRIQDNLE 244 Query: 275 RVA-AWAKARGLGHHPPEGTYLAWIQT--PFPKAAAYFLERARVALNPGESFG-RGYDTY 330 A A + + P GTYL W+Q ++AA + RA V ++ GE+F +G + Sbjct: 245 TAAEALVRTGRMRTSVPAGTYLLWVQVLGLGAESAAAWARRAGVVVSAGETFDLQGRSDW 304 Query: 331 VRLNFATYPEVLEEALRRLDG 351 +R+N AT PEVL E L RL G Sbjct: 305 MRVNVATEPEVLAEMLDRLVG 325 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: 353 Number of extensions: 23 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: 354 Length of database: 329 Length adjustment: 29 Effective length of query: 325 Effective length of database: 300 Effective search space: 97500 Effective search space used: 97500 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: 49 (23.5 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