Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 (characterized)
to candidate RR42_RS30610 RR42_RS30610 cystathionine beta-lyase
Query= SwissProt::Q07703 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS30610 Length = 405 Score = 332 bits (850), Expect = 2e-95 Identities = 183/385 (47%), Positives = 243/385 (63%), Gaps = 7/385 (1%) Query: 11 TLLQHLGSAPFNPDTGAAPVNLPSVRASTVRFQSLAKLEDAQRRKAAGERASTYGRMGMD 70 T L H G A + G PVN P VRASTV F S+A++ + + R+ + ER TYG G Sbjct: 7 THLAHAGRA--SAVDGGQPVNPPVVRASTVLFDSVAQMREMRSRRGS-ERLFTYGARGNP 63 Query: 71 THAALEQVFAELEGGTHCYLASSGLAGISMVFLSLLSAGEHALVADCAYGPVHELHEAVL 130 T ALE + ELE G L SGLA +M L+ L G+H L+ DC Y PV +L E L Sbjct: 64 TAFALEDMVTELEAGYRTRLFPSGLAAAAMTLLAYLRPGQHVLLPDCVYEPVRKLAEGFL 123 Query: 131 SRLGIDVTFFDAKA-DLASLVRPTTRLIFAEAPGSLLFEMLDMPALARFAKQHDLILATD 189 ++ GI +F+ A DL + +R TRL++ EAPGSL +EM D+PA+A A +H ++A D Sbjct: 124 AQHGIAASFYAADGHDLQARLRRETRLVYVEAPGSLAYEMCDLPAIADIAHRHGALVAAD 183 Query: 190 NTWGSGYIYRPLTLGAQVSVIAGTKYVGGHSDLMLGAVVTNDEAIAKRLNRTQYALGYSV 249 NTWGSG +Y+PL LGA +S++A TKY+ GHSD+M+G V T EA L A G SV Sbjct: 184 NTWGSGLLYQPLALGADISLMAATKYLSGHSDVMMGTVCTL-EAAWPALAAVADAFGISV 242 Query: 250 SADDAWLALRGVRTMPVRMAQHARHALEVCEFLQNRPEVVRLYHPAWPADPGHALWQRDC 309 S DDA+L RG+R++ R++QH R AL V +L+ RPEV ++ PA P DPGHALWQRDC Sbjct: 243 SPDDAYLVQRGMRSLGARLSQHERSALAVAHWLRTRPEVAEVFCPALPGDPGHALWQRDC 302 Query: 310 SGSNGMLAVQL-GLSPQAARDFVNALTLFGIGFSWGGFESLVQLVTPGELARHQYWQGGS 368 G+NG+L+ L ++P AA F+++L LFGIG SWGGFESL + W G Sbjct: 303 HGTNGLLSFALRAVAPDAAERFIDSLALFGIGASWGGFESLAVIADMRGARSVTDWSGRG 362 Query: 369 DALVRLHIGLESPADLIADLAQALD 393 ++RLHIGLE DL+ADLA+ + Sbjct: 363 Q-VIRLHIGLEDVDDLLADLARGFE 386 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: 453 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: 396 Length of database: 405 Length adjustment: 31 Effective length of query: 365 Effective length of database: 374 Effective search space: 136510 Effective search space used: 136510 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