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_027457073.1 K420_RS0104895 putative C-S lyase
Query= SwissProt::Q08432 (387 letters) >NCBI__GCF_000519045.1:WP_027457073.1 Length = 376 Score = 238 bits (607), Expect = 2e-67 Identities = 140/386 (36%), Positives = 209/386 (54%), Gaps = 16/386 (4%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 + D +R G+ S KW K + D LP+WVADMDF AP A+ AL R++HG+FGY Sbjct: 3 SLDTPVDRRGSDSFKWGK----YAGRDILPLWVADMDFAAPPAVLAALHRRIEHGVFGYG 58 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 P +V +Q+ +GW + PE + + PG+VT L++A +A V+ P+Y P Sbjct: 59 GPWPSLTASVLAHLQDEYGWTIEPEWLVWLPGLVTGLNVACRAV---DGAVLTATPIYPP 115 Query: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRED 181 F +GR + L D + D ++ + + + LF+LC+PHNP GR WSR++ Sbjct: 116 FLSAPHFSGRKLNRVELARDDNRWHWDMAAMQ-QATTAATRLFLLCHPHNPVGRCWSRDE 174 Query: 182 LLKLGELCLEHGVTVVSDEIHSDLMLYGHK-HTPFASLSDDFADISVTCAAPSKTFNIAG 240 LL L + H + V SDEIH L+L K H PFASLS + A S+T APSKTFNI G Sbjct: 175 LLALADYAERHDLVVCSDEIHCGLILDPDKRHIPFASLSPEIAQRSITLMAPSKTFNIPG 234 Query: 241 LQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNMN 300 L + +IP+ R +F ++ + +N + A EAA+ GG W +LITY+ N + Sbjct: 235 LGCAFAVIPNPALRRQFERAM-HGIVPHVNVLGLAACEAAFRDGGDWHRDLITYLRGNRD 293 Query: 301 EAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGG 360 A + + LP ++M +A+YL W+D L++ + + L G + G Sbjct: 294 RVSASIGS-LPGLRMAPVEATYLAWIDVRDLCLANPAAH---FEAHGIGLSDGADF--GA 347 Query: 361 EGFMRLNAGCSLATLQDGLRRIKAAL 386 G++RLN GC ATL + L R + A+ Sbjct: 348 PGWLRLNFGCPRATLDEALARFERAV 373 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: 431 Number of extensions: 23 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: 387 Length of database: 376 Length adjustment: 30 Effective length of query: 357 Effective length of database: 346 Effective search space: 123522 Effective search space used: 123522 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