Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_086508963.1 BZY95_RS05445 putative C-S lyase
Query= SwissProt::Q5SHW0 (354 letters) >NCBI__GCF_002151265.1:WP_086508963.1 Length = 392 Score = 225 bits (573), Expect = 2e-63 Identities = 162/379 (42%), Positives = 199/379 (52%), Gaps = 41/379 (10%) Query: 9 SLKWGTYPEDVLPLWVADMDFPPAEAIQQALAERA-RGFLGYP--PREGDRELRELILEA 65 S KW Y +LPLWVADMDFP + +AL R G GY P + L E Sbjct: 21 SQKWHRYDASILPLWVADMDFPSPPQVIEALKARVDHGVFGYGTVPDSLKQTLCEWSSRE 80 Query: 66 LGLEAE---LAFMPGVVVGLYAAVAAFTAPGQGVLTQVPIYPPFLAAI----RDQRRTVL 118 G E ++PGVV L+ A A T PG GVLT PIYPPFL R ++ L Sbjct: 81 YGWAIEPEWQLWLPGVVPALHVASLALTEPGDGVLTLTPIYPPFLKVAERTGRLSQQVAL 140 Query: 119 ANPLRETPEGYRLDLAGLER-LAFATRLLLFCHPHNPTGRVFGEEELAALAQIARRHDLI 177 A P E +RLDLA LE + TRLLL+C PHNPTGRV+ EELA LA + RHDL+ Sbjct: 141 AEPAGPG-EPWRLDLAALEAAITPETRLLLWCQPHNPTGRVWRHEELAGLAALIERHDLL 199 Query: 178 VVSDELHAPLTYEK--PHVPLARFLPE---RTLTLVGPGKTYNLAGLPIGAVLGP----- 227 VVSDELH L ++ H PLA PE R +TL P KT+NLAGL + P Sbjct: 200 VVSDELHCDLLLDEGARHRPLAAAFPELAARIITLWAPSKTFNLAGLTAACAVIPNGELR 259 Query: 228 KPLVEAVKRHLPHVFPNVLAMAAWKAALKEGGPWLKATLEQLRANR----DRVAAWAKAR 283 + A + LP V NVL + A + A + W +A L+ LR +R +RVA W Sbjct: 260 QRFAAAARGLLPDV--NVLGLVAAEVAYGQCNAWRQALLKTLRGHRQVLIERVAQWP--- 314 Query: 284 GLGHHPPEGTYLAWIQTPFPKAAA--------YFLERARVALNPGESFGRGYDTYVRLNF 335 G+G PE TYLAW+ + A L+ A+VAL+ G F G+ +VRLNF Sbjct: 315 GVGMSVPEATYLAWLDMRRAEGLAQRQGSPQQLLLQEAKVALSDGADF--GWPGFVRLNF 372 Query: 336 ATYPEVLEEALRRLDGALK 354 T LE AL RLDG LK Sbjct: 373 GTTASQLEAALARLDGVLK 391 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: 497 Number of extensions: 33 Number of successful extensions: 7 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: 392 Length adjustment: 30 Effective length of query: 324 Effective length of database: 362 Effective search space: 117288 Effective search space used: 117288 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