Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 (characterized)
to candidate RR42_RS31610 RR42_RS31610 cystathionine beta-lyase
Query= SwissProt::Q07703 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS31610 Length = 402 Score = 421 bits (1081), Expect = e-122 Identities = 210/387 (54%), Positives = 280/387 (72%), Gaps = 5/387 (1%) Query: 8 HIDTLLQHLGSAPFNPDTGAAPVNLPSVRASTVRFQSLAKLEDAQRRKAAGERASTYGRM 67 H DT L H G+ PF G PVN+P VR STVRF++ +D + R A GER S+YGR Sbjct: 4 HRDTQLIHAGTPPFVQ--GHGPVNVPVVRTSTVRFENSDAYDDIRARHARGERVSSYGRH 61 Query: 68 GMDTHAALEQVFAELEGGTHCYLASSGLAGISMVFLSLLSAGEHALVADCAYGPVHELHE 127 GMDTH ALE A LEGG +LA SGLA IS+ FL+LLS G+HALV D Y PV L + Sbjct: 62 GMDTHRALEDAIAGLEGGNRAFLAPSGLAAISLTFLALLSPGDHALVVDSVYAPVRRLEQ 121 Query: 128 AVLSRLGIDVTFFD-AKADLASLVRPTTRLIFAEAPGSLLFEMLDMPALARFAKQHDLIL 186 +L RLGI+V++F ++ DL +L+RP TRL++ E+P SLL+E+LD+P L + A +H +++ Sbjct: 122 TLLRRLGIEVSYFSPSQDDLDALIRPNTRLLYLESPSSLLYEVLDLPRLVQIAHRHGVVV 181 Query: 187 ATDNTWGSGYIYRPLTLGAQVSVIAGTKYVGGHSDLMLGAVVTNDEAIAKRLNRTQYALG 246 ATDNTW SG+ +PL LG +S++A TKY+ GHSDLM GAVV DEA+A+R+ G Sbjct: 182 ATDNTWASGHALQPLALGVDISILASTKYISGHSDLMQGAVVVKDEALARRIADAHDGFG 241 Query: 247 YSVSADDAWLALRGVRTMPVRMAQHARHALEVCEFLQNRPEVVRLYHPAWPADPGHALWQ 306 ++SADDA+LALRG+RT+ VR+AQH R+AL V +FL+ V R+++PA P+DPGHALW Sbjct: 242 LAISADDAYLALRGIRTLAVRLAQHQRNALAVAQFLEAHEAVGRVFYPALPSDPGHALWL 301 Query: 307 RDCSGSNGMLAVQLGLSP-QAARDFVNALTLFGIGFSWGGFESLVQLVTPGELARHQYWQ 365 RD SG+NG+++ L + AAR V++L+LFG+G SWGG+ESLVQ+ P LA H YW+ Sbjct: 302 RDFSGANGLVSFSLPTADVAAARKLVDSLSLFGLGASWGGYESLVQVAAPERLAEHSYWR 361 Query: 366 GGSDALVRLHIGLESPADLIADLAQAL 392 G++ ++RLHIGLE+P DLIADLAQ L Sbjct: 362 -GAEPVIRLHIGLEAPEDLIADLAQGL 387 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: 473 Number of extensions: 22 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: 402 Length adjustment: 31 Effective length of query: 365 Effective length of database: 371 Effective search space: 135415 Effective search space used: 135415 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