Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_007056294.1 BL_RS07855 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::Q93QC6 (368 letters) >NCBI__GCF_000007525.1:WP_007056294.1 Length = 417 Score = 222 bits (566), Expect = 1e-62 Identities = 128/382 (33%), Positives = 203/382 (53%), Gaps = 21/382 (5%) Query: 6 LEELKNRRTLKWTRFPEDVLPLWVAESDFGTCPQLKEAMADAVEREVFGYPPDATGLNDA 65 +E+L+ + KWTR+P + ++AE D+G P + EA+ +A ER GY PD A Sbjct: 32 IEDLEQVGSDKWTRYP-GCIGAFIAEMDYGLAPCVAEAIEEATERGALGYIPDPWKKEVA 90 Query: 66 LT-GFYERRYGFGPNPESVFAIPDVVRGLKLAIEHFTKPGSAIIVPLPAYPPFIELPKVT 124 + ++RRYG+ +P + +PDV+ ++ + + G++I+VP PAY PF+ +P++ Sbjct: 91 RSCAAWQRRYGWEVDPTCIRPVPDVLEAFEVFLREIVRAGNSIVVPTPAYMPFLSVPRLY 150 Query: 125 GRQAIYI--------------DAHEYDLKEIEKAFADGAGSLLFCNPHNPLGTVFSEEYI 170 G + + I D +D IE+AFA+G + + CNPHNP+G V + E + Sbjct: 151 GVEVLEIPMLCAGAGESSGRNDEWLFDFDAIEQAFANGCHAFVLCNPHNPIGKVLTREEM 210 Query: 171 RELTDIAAKYDARIIVDEIHAPLVYEG-THVVAAGVSENAANTCITITATSKAWNTAGLK 229 L+D+AAKYD RI DEIHAP VY+G THV A ++ A T T+ SK++N G K Sbjct: 211 LRLSDLAAKYDVRIFSDEIHAPFVYQGHTHVPFASINRQTAMQAFTSTSASKSFNIPGTK 270 Query: 230 CAQIFFSNEADVKAWKNLSDITRDGVSILGLIAAETVYNEGEEFLDESIQILKDNRDFAA 289 CAQ+ +N D++ W ++ + + +G IA Y+ G + + + ++ N Sbjct: 271 CAQVILTNPDDLELWMRNAEWSEHQTATIGAIATTAAYDGGAAWFEGVMAYIERNIALVN 330 Query: 290 AELEKLGVKV--YAPDSTYLMWLDFAGTKIEEAPSKILREEGKVMLNDGAAFGGF-TTCA 346 ++ KV P TY+ WLDF+ I + P+ ++ V L DG G C Sbjct: 331 EQMRTRFAKVRYVEPQGTYIAWLDFSPLGIGD-PANYFFKKANVALTDGRECGEVGRGCV 389 Query: 347 RLNFACSRETLEEGLRRIASVL 368 R+NFA LEE R+A+ L Sbjct: 390 RMNFAMPYPLLEECFDRMAAAL 411 Lambda K H 0.319 0.137 0.408 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: 401 Number of extensions: 22 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: 368 Length of database: 417 Length adjustment: 31 Effective length of query: 337 Effective length of database: 386 Effective search space: 130082 Effective search space used: 130082 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 12 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