Align Cystathionine beta-lyase PatB; CBL; Beta-cystathionase PatB; Cysteine lyase PatB; Cysteine-S-conjugate beta-lyase PatB; EC 4.4.1.13 (characterized)
to candidate WP_029910020.1 P166_RS0106405 putative C-S lyase
Query= SwissProt::Q08432 (387 letters) >NCBI__GCF_000711315.1:WP_029910020.1 Length = 398 Score = 287 bits (734), Expect = 4e-82 Identities = 158/393 (40%), Positives = 224/393 (56%), Gaps = 9/393 (2%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 +F++ R T + K+ LFG D LPMWVADMD P I +A+K RL+H I GYT Sbjct: 3 DFNRVFPREDTDAEKYALRKALFGREDILPMWVADMDLPTPNFIMQAIKTRLEHPILGYT 62 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 + A+ W Q H ++V E I F+ V MAVQAFT+ G+ V+ PPVY P Sbjct: 63 HMSEAVYQAIIDW-QAFHEYEVKSEEIVFTHNVANGFFMAVQAFTKAGEAVLAMPPVYPP 121 Query: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRED 181 F E NGR ++ PL+ K+G Y IDF+ LE+K+ + V L + C+P NPSGR W+ + Sbjct: 122 FLTAPELNGRKLVTAPLVLKNGRYEIDFDLLESKIVENKVQLILFCHPQNPSGRVWTENE 181 Query: 182 LLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAGL 241 L KL E+C+ H VT+VSDEIHSD M++ KH P A++SD ++T ++P KTFN+ GL Sbjct: 182 LKKLAEICVTHKVTIVSDEIHSD-MIFSGKHIPLATISDAIRQQTITLSSPGKTFNLGGL 240 Query: 242 QASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYS-KGGPWLDELITYIEKNMN 300 Q II + +A + Q + GLN FA A+EAAYS KG ++ EL ++++N++ Sbjct: 241 QIGYAIIANPKLKAAYLKVSQSVSVKGLNLFATVALEAAYSEKGRRYVQELNQFLQQNID 300 Query: 301 EAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYG--- 357 + F T P+V +M+P+ASYL+WLDFS A L+ ++ K+ L G + Sbjct: 301 KTVDFFQTHFPQVTVMRPEASYLVWLDFSTLCSDHAALKNWIINDAKLGLNDGESFDVKT 360 Query: 358 ---PGGEGFMRLNAGCSLATLQDGLRRIKAALS 387 G FMR+N LQ K L+ Sbjct: 361 DKPNAGTCFMRMNLAVPPRVLQQAFSHFKMGLN 393 Lambda K H 0.318 0.135 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: 421 Number of extensions: 16 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: 398 Length adjustment: 31 Effective length of query: 356 Effective length of database: 367 Effective search space: 130652 Effective search space used: 130652 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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