Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 (characterized)
to candidate HSERO_RS14995 HSERO_RS14995 cystathionine beta-lyase
Query= SwissProt::Q07703 (396 letters) >FitnessBrowser__HerbieS:HSERO_RS14995 Length = 392 Score = 247 bits (630), Expect = 5e-70 Identities = 146/363 (40%), Positives = 207/363 (57%), Gaps = 12/363 (3%) Query: 37 ASTVRFQSLAKLEDAQRRKAAGERASTYGRMGMDTHAALEQVFAELEGGTHCYLASSGLA 96 ASTV F +A + R+ G TYG G T LE AE+EGG +C + SGLA Sbjct: 36 ASTVLFPDVAAMRSRDWREKLGY---TYGLHGTPTSFVLEARLAEIEGGKYCRVTPSGLA 92 Query: 97 GISMVFLSLLSAGEHALVADCAYGPVHELHEAVLSRLGIDVTFFDAKAD--LASLVRPTT 154 I+MV + L +G+ L+ D YGP +L + + I F+D LA L+RPTT Sbjct: 93 AIAMVNFAFLKSGDDVLLPDNVYGPSKDLGQWLERDFQITARFYDPMIGEGLAELIRPTT 152 Query: 155 RLIFAEAPGSLLFEMLDMPALARFAKQHDLILATDNTWGSGYIYRPLTLGAQVSVIAGTK 214 RL++ EAPGS+ E+ D+PAL R A +++A DNTW +G ++ G + + A TK Sbjct: 153 RLVWTEAPGSVSMEVPDIPALCRAAHAKGVLVAIDNTWSAGIAFKAFEHGVDIVMQAVTK 212 Query: 215 YVGGHSDLMLGAVVTNDEAIAKRLNRTQYALGYSVSADDAWLALRGVRTMPVRMAQHARH 274 Y G SD+++GAV+ D+A+ ++L LG+ V DD ++ LR + +M +R H Sbjct: 213 YQSGGSDVLMGAVIVRDQALNEKLELAHMRLGFGVGMDDVYMVLRSLSSMRLRFEAHDAA 272 Query: 275 ALEVCEFLQNRPEVVRLYHPAWPADPGHALWQRDCSGSNGMLAVQLG---LSPQAARDFV 331 A +V +L+ RPE+V + HPA+ PGHA W+RD SG+ G+ +V + Q R FV Sbjct: 273 ARKVAAWLKQRPEIVAVLHPAFEDCPGHAHWKRDFSGAGGLFSVIFDPRYVEAQTDR-FV 331 Query: 332 NALTLFGIGFSWGGFESLVQLVTPGELARHQYWQGGSDALVRLHIGLESPADLIADLAQA 391 ++L LF IG+SWGG SL + R +G LVR +IGLESP DLIAD+ QA Sbjct: 332 DSLRLFKIGYSWGGAHSLCVPYRMKGMRRAWMREG---QLVRFNIGLESPEDLIADIEQA 388 Query: 392 LDR 394 L R Sbjct: 389 LAR 391 Lambda K H 0.321 0.134 0.403 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: 386 Number of extensions: 16 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: 396 Length of database: 392 Length adjustment: 31 Effective length of query: 365 Effective length of database: 361 Effective search space: 131765 Effective search space used: 131765 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 (21.9 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