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_019557492.1 F612_RS0109285 putative C-S lyase
Query= SwissProt::Q08432 (387 letters) >NCBI__GCF_000381085.1:WP_019557492.1 Length = 400 Score = 302 bits (773), Expect = 1e-86 Identities = 154/380 (40%), Positives = 220/380 (57%), Gaps = 2/380 (0%) Query: 9 RLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYTTPDQKTK 68 R G+ + K+ LFG D LPMWVADMD P I +ALK+RL H + GYT + Sbjct: 18 REGSYAEKYALREALFGTEDVLPMWVADMDLPTPSFILDALKKRLQHPLLGYTVTPEPVY 77 Query: 69 DAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTPFYHMVEK 128 A+ W Q H + + I F+ V MAV AFT+PGD V+VQPP+Y PF + Sbjct: 78 QAIIDW-QAHHHYHITTSQIVFTHNVANGFHMAVSAFTQPGDSVLVQPPIYPPFLQAPKL 136 Query: 129 NGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSREDLLKLGEL 188 N R ++ PL+ + Y IDF ET + D V LF+ CNPHNP GR W R +L ++ E+ Sbjct: 137 NDRTLVETPLVRLNHQYQIDFAAFETAIVDNQVKLFLFCNPHNPVGRVWLRSELEQIAEI 196 Query: 189 CLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAGLQASAIII 248 C+ H V +VSDEIHSDL+ G +H P ASLS + A+I+VT ++P KTFN+ GLQ +I Sbjct: 197 CVRHNVIIVSDEIHSDLVYDGQQHVPIASLSPEVANITVTLSSPGKTFNLGGLQIGYALI 256 Query: 249 PDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGG-PWLDELITYIEKNMNEAEAFLS 307 + + + + + LN FA+ A+++AYSK G W ++L+ + +N++ E F+ Sbjct: 257 ANPQLKTAYLSIANSVSIHNLNLFAMIALQSAYSKQGFTWKEDLLKHFTQNLDTVENFVK 316 Query: 308 TELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGGEGFMRLN 367 LP V +P ASYLIWLDF L+ +++K K+ L G +G G+GFMR+N Sbjct: 317 EFLPLVTFSRPQASYLIWLDFREMFDDQETLKNWLVQKAKLGLNDGLAFGEAGKGFMRMN 376 Query: 368 AGCSLATLQDGLRRIKAALS 387 S L L++++ A S Sbjct: 377 IAVSKPALLKALKQLETAAS 396 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: 450 Number of extensions: 19 Number of successful extensions: 3 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: 400 Length adjustment: 31 Effective length of query: 356 Effective length of database: 369 Effective search space: 131364 Effective search space used: 131364 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