Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate CA265_RS08190 CA265_RS08190 cystathionine gamma-synthase
Query= SwissProt::Q83A83 (387 letters) >FitnessBrowser__Pedo557:CA265_RS08190 Length = 371 Score = 314 bits (805), Expect = 2e-90 Identities = 166/377 (44%), Positives = 234/377 (62%), Gaps = 11/377 (2%) Query: 12 DTRVIHAGQKPDPLTGAVMTPIYTASTYAQKSPGVHQG-YEYSRSQNPTRFAYERCVADL 70 +T IHA +TG V P+ ++T+ + + G + G + YSR NP R A E VA L Sbjct: 4 ETLAIHASNLVKSITGDVTPPLNLSTTFFRDAEGGYPGGHMYSRVSNPNRSALENTVAKL 63 Query: 71 ESGQHGFAFASGMAATATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSAGLSFSFVDF 130 E G+ AF+SG + + L+PG H++ DD+Y G + + S L F F+D Sbjct: 64 EYGEDAAAFSSGNTCGLVLFQALKPGSHIIAPDDMYWGIKKQLLTIFNDS--LEFDFIDQ 121 Query: 131 TDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTFATPIIQRP 190 TD + ++ ++ + TK++W+E+PSNP LK+ D+ +IA+IAK KNI D+TFA+PI+Q P Sbjct: 122 TDLDLIQASIRSNTKLIWIETPSNPLLKVTDIEEIAKIAKAKNITLACDSTFASPILQNP 181 Query: 191 LELGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLKYLQNAIGAIAAPFDSFMVLR 250 + LG DIV HS+TKYL GHSD++GG+ V L E++K +Q GA+ +PFD F++ R Sbjct: 182 ILLGADIVMHSSTKYLGGHSDVLGGILVTAKKDELWEKIKNIQQTGGAVPSPFDCFLLTR 241 Query: 251 GLKTLAIRMERHCENAMQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMRYFGGMISVE 310 +KTLA RM+ HCEN +A +L HP V+ V+YPGL SHPQH IAKKQM+ FGGM+S Sbjct: 242 SIKTLAYRMKGHCENGKIIADYLNAHPNVEAVFYPGLESHPQHDIAKKQMKDFGGMMSFL 301 Query: 311 LKCDLNETKKVLERCQLFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLS 370 +K D+ KV+ + QLF A SLGGVESLIEH P ++ K +R+S Sbjct: 302 VKGDVEAAHKVVNKVQLFAQATSLGGVESLIEH---RYSVEGPDSKTPK-----NLLRIS 353 Query: 371 VGIEAITDLRHDLEAAL 387 VG+E D+ DL AL Sbjct: 354 VGLEHADDIIADLAQAL 370 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: 412 Number of extensions: 12 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: 371 Length adjustment: 30 Effective length of query: 357 Effective length of database: 341 Effective search space: 121737 Effective search space used: 121737 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 09 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