Align Putative cystathionine beta-lyase; CBL; EC 4.4.1.13; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; ORF5 (uncharacterized)
to candidate BPHYT_RS09190 BPHYT_RS09190 cystathionine beta-lyase
Query= curated2:Q52811 (396 letters) >FitnessBrowser__BFirm:BPHYT_RS09190 Length = 394 Score = 297 bits (761), Expect = 3e-85 Identities = 164/367 (44%), Positives = 223/367 (60%), Gaps = 9/367 (2%) Query: 34 PVVHASTVLFPNARAMETRTQK----YTYGTRGTPTTDALCEAIDALEGSAGTILVPSGL 89 PV ASTV+FP+ M K + YG TPT+ AL + + +EG +L PSGL Sbjct: 31 PVTRASTVVFPDLATMRALDWKNDAQWRYGLHATPTSLALAQRLATIEGGNHALLQPSGL 90 Query: 90 AAVTIPFLGFVAAGDHALVVDSVYGPTRHFCDTMLKRLGVEVEYYHPEIGAGIETLFRSN 149 ++++ + G V AGD L+ D+VY P R D + + G+ V YY P IGAG+ L + N Sbjct: 91 SSISNVYFGLVKAGDDVLIPDNVYSPNRDHGDWLARDFGITVRYYDPMIGAGMADLIQPN 150 Query: 150 TKLVHTEAPGSNTFEMQDIPAISAVAHRHGAVVMMDNTWATPVYFRPLDHGVDISIHAST 209 T+L+ EAPGS T E+ D+PAI+A A V +DNTW+ + FRP DHGVDIS+ A T Sbjct: 151 TRLIWLEAPGSVTMEVADVPAITAAARARNVVTAIDNTWSAGLGFRPFDHGVDISVQALT 210 Query: 210 KYPSGHSDILLG-TVSANAEHWERLKEANGVLGICGAPDDAYQILRGLRTMGLRLERHYE 268 KY SG D+L+G T++ + E +LK A +GI + DD ILR L TM LR E+H Sbjct: 211 KYQSGGGDVLMGATITVDRELHLKLKAARMRMGIGVSSDDCSLILRSLPTMQLRFEQHDR 270 Query: 269 SALDIAKWLEGRDDVARVLHPALPSFPSHHLWKRDFKGASGIFSFVLAADGPEKSRAKAH 328 SAL +AKWL+ R ++A VLHPAL P H +KRDF GA G+FS V DG S A+ Sbjct: 271 SALGLAKWLKTRPEIAAVLHPALSDCPGHEFYKRDFTGAGGLFSVVF--DG-RYSPAQID 327 Query: 329 AFLDALRIFGLGYSWGGFESLAL-HAYLNDRTVAKAPTDGPVIRLQIGIEDVADLKADIE 387 F ++L +F LG+SWGG SLA+ + + RT + P G ++R IG+E ADL+AD+E Sbjct: 328 TFCESLELFSLGWSWGGAHSLAMPYDVASMRTAGQWPHSGTLVRFYIGLEAEADLRADME 387 Query: 388 RGFAAAS 394 + A S Sbjct: 388 QSLARLS 394 Lambda K H 0.320 0.137 0.417 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: 406 Number of extensions: 15 Number of successful extensions: 5 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: 396 Length of database: 394 Length adjustment: 31 Effective length of query: 365 Effective length of database: 363 Effective search space: 132495 Effective search space used: 132495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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