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_011767103.1 AZO_RS16965 putative C-S lyase
Query= SwissProt::Q08432 (387 letters) >NCBI__GCF_000061505.1:WP_011767103.1 Length = 380 Score = 259 bits (662), Expect = 9e-74 Identities = 146/387 (37%), Positives = 213/387 (55%), Gaps = 13/387 (3%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 +FD+ +R KW + + D LP+WVADMDF AP + EAL+ RLDHG+FGYT Sbjct: 4 DFDRHPDRRQVPGEKWGR----YAGRDVLPLWVADMDFSAPPPVLEALRRRLDHGVFGYT 59 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 +AV ++ H W + PE + + PGVVT ++A +A E GD V PVY P Sbjct: 60 DAPPSLAEAVVEGLRRDHDWHIQPEWLVWLPGVVTGFNLACRAVGEAGDSVFTATPVYPP 119 Query: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRED 181 F E +GR ++ L+E++G + D +E + +P +F+LCNPHNP GR++ RE+ Sbjct: 120 FLTAPENSGRRLVSCALVERNGRWEWDRAAVEAAI-EPRTRVFMLCNPHNPVGRAFDREE 178 Query: 182 LLKLGELCLEHGVTVVSDEIHSDLML-YGHKHTPFASLSDDFADISVTCAAPSKTFNIAG 240 L + +L + V SDEIH L+L H P A+L + A S+T APSKT+NI Sbjct: 179 LRWIADLAESRDLVVCSDEIHCGLVLDAARPHLPIAALDERIARRSITLMAPSKTWNIPA 238 Query: 241 LQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNMN 300 L + +IPD R ++ + R + +N + A EAAY GGPW L+ Y+ N Sbjct: 239 LYCAFAVIPDAGLRRRYQREM-RGIVPHVNVMGLVAAEAAYRHGGPWRAALLDYLRDNRE 297 Query: 301 EAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGG 360 ++T +P ++ +P+A+YL W+D GL D + G V L G +G Sbjct: 298 RVLDAVAT-MPGLRTTRPEATYLAWIDCRDAGLDD---PAAFFEAGGVGLSDGRAFGM-- 351 Query: 361 EGFMRLNAGCSLATLQDGLRRIKAALS 387 GF+RLN GCS ATL + L R++ AL+ Sbjct: 352 PGFVRLNFGCSRATLDEALARMRRALT 378 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: 459 Number of extensions: 26 Number of successful extensions: 6 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: 380 Length adjustment: 30 Effective length of query: 357 Effective length of database: 350 Effective search space: 124950 Effective search space used: 124950 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