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_024851555.1 N745_RS0107740 putative C-S lyase
Query= SwissProt::Q08432 (387 letters) >NCBI__GCF_000526715.1:WP_024851555.1 Length = 398 Score = 293 bits (751), Expect = 4e-84 Identities = 157/392 (40%), Positives = 227/392 (57%), Gaps = 9/392 (2%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 +F++ R G+ + K++ LFG D LPMWVADMD P+ I +A+K RL+H I GYT Sbjct: 3 DFNRVFPREGSDAEKYELRKTLFGRDDVLPMWVADMDLPTPDFIMQAIKTRLEHPILGYT 62 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 + W Q H ++V PE I F+ V MAVQAFT+P + V+V PPVY P Sbjct: 63 HMSDSVYKCIIDW-QAYHDYEVKPEHILFTHNVANGFFMAVQAFTKPKEAVLVMPPVYPP 121 Query: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRED 181 F E N R ++ PL+ + G Y IDFE L+ K+ + V L + C+PHNPSGR W +++ Sbjct: 122 FLTAPEINDRKLVTAPLVLEAGRYEIDFEALQKKIVENKVKLILFCHPHNPSGRVWQQDE 181 Query: 182 LLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAGL 241 L KL ++C+EH V +VSDEIHSD++ G +H P ASLSD+ +++T ++P K FN+ GL Sbjct: 182 LEKLAKICIEHQVVIVSDEIHSDMVFVG-RHIPLASLSDEIKQLTITLSSPGKIFNLGGL 240 Query: 242 QASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYS-KGGPWLDELITYIEKNMN 300 Q II + +A + Q + LN FA AI+ AYS KG ++ EL ++++N++ Sbjct: 241 QIGYAIIANAKLKAAYLKVAQSVSIKELNLFAAVAIKIAYSEKGRRYVQELNQFLQQNID 300 Query: 301 EAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYG--- 357 + EAF T P+VK+M+P+ASYL+WLDFS L+ ++ + K+ L G + Sbjct: 301 KTEAFFQTHFPQVKVMRPEASYLVWLDFSTMCTKHETLKDWVVNEAKLGLNDGESFDVKS 360 Query: 358 ---PGGEGFMRLNAGCSLATLQDGLRRIKAAL 386 G FMR+N LQ K L Sbjct: 361 NRPNAGSCFMRMNLAVPPRVLQQAFSHFKMGL 392 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: 418 Number of extensions: 19 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