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 GFF84 PGA1_c00860 cystathionine beta-lyase PatB
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__Phaeo:GFF84 Length = 390 Score = 295 bits (754), Expect = 2e-84 Identities = 150/390 (38%), Positives = 223/390 (57%), Gaps = 6/390 (1%) Query: 1 MNFDKREERLGTQSVKWDKTGELFGVT--DALPMWVADMDFRAPEAITEALKERLDHGIF 58 MNFDK +R T +KWD +L+ V + L MWVADMDF P +T+ ++E DHG++ Sbjct: 1 MNFDKIIDRRNTHCIKWDMMEDLYNVPRDEGLSMWVADMDFAVPSVVTDKMREMADHGVY 60 Query: 59 GYTTPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPV 118 GY D K A+C WMQNRHGW V+PE+I + G+V + M + FT+ GD +V+ PV Sbjct: 61 GYVNCDSPYKSAICWWMQNRHGWSVDPEAIFTTTGLVNGVGMCLDTFTQQGDGIVLFTPV 120 Query: 119 YTPFYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWS 178 Y F ++ GR ++ L DG Y +DF + +++ + + ILC+PHNP GR W+ Sbjct: 121 YHAFAKVIRNAGREVVECELAVNDGRYEMDFSTYDAQMTG-AEKMVILCSPHNPVGRVWT 179 Query: 179 REDLLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNI 238 E+L + + H + ++SDEIH DL+ G H P + + D D + APSKTFN Sbjct: 180 EEELRGVADFAKRHDLILLSDEIHHDLVFDGATHIPMQNAAPDITDRLLMLTAPSKTFNF 239 Query: 239 AGLQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYS-KGGPWLDELITYIEK 297 AG+ +IIPD RAKFS + L N+ A AAYS +G W+DEL+ Y++ Sbjct: 240 AGMHTGQVIIPDPELRAKFSRRMMALALSP-NSPGQWATAAAYSPEGAAWVDELVPYLDG 298 Query: 298 NMNEAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYG 357 N +A ++ E+P + + +A+YL W+DFS G+S E R+ + K+ G +G Sbjct: 299 NRQLFDAAVN-EIPGLHSTRLEATYLAWVDFSGTGMSREEFTARVEQGAKIAANHGPSFG 357 Query: 358 PGGEGFMRLNAGCSLATLQDGLRRIKAALS 387 GGE F+R N G A +++ R++ A S Sbjct: 358 TGGENFLRFNLGTQRARVEEACDRLRNAFS 387 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: 468 Number of extensions: 21 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: 390 Length adjustment: 30 Effective length of query: 357 Effective length of database: 360 Effective search space: 128520 Effective search space used: 128520 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 09 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