Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; Osteotoxin; EC 4.4.1.13 (characterized)
to candidate RR42_RS07655 RR42_RS07655 cystathionine beta-lyase
Query= SwissProt::Q07703 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS07655 Length = 392 Score = 267 bits (682), Expect = 4e-76 Identities = 161/380 (42%), Positives = 223/380 (58%), Gaps = 19/380 (5%) Query: 26 GAAPVNLPSVRASTVRFQSLAKLEDAQRRKAAGERASTYGRMGMD---THAALEQVFAEL 82 G A + + R STV F++LA+L +A G+ A+TY R G+ T AL Q A + Sbjct: 15 GFASFSQATHRGSTVVFRNLAEL------RAHGDGATTYWRYGLHATPTSEALCQHLALI 68 Query: 83 EGGTHCYLASSGLAGISMVFLSLLSAGEHALVADCAYGPVHELHEAVLSRLGIDVTFFDA 142 EG H L SGLA IS V+ +L+ +G+ LV D YGP E E + G+ V ++D Sbjct: 69 EGARHALLLPSGLAAISQVYFALVKSGDDVLVPDNVYGPNREHGEWLARDFGVSVRYYDP 128 Query: 143 K--ADLASLVRPTTRLIFAEAPGSLLFEMLDMPALARFAKQHDLILATDNTWGSGYIYRP 200 A +A L+R TRLI+ E+PGS+ E+ D A+ AK ++ A DNTW +G +RP Sbjct: 129 MIGAGIAGLIRSNTRLIWMESPGSVTMEIPDTEAIVAAAKARGVLTAIDNTWSAGVYFRP 188 Query: 201 LTLGAQVSVIAGTKYVGGHSDLMLGAVVTNDEAIAKRLNRTQYALGYSVSADDAWLALRG 260 G +SV A TKY G SD+++GAV++ D+ + R+ R + +G+ VSADD +L LR Sbjct: 189 FDKGIDISVQALTKYQSGGSDVLMGAVLSTDDKLHDRIKRARMLMGWGVSADDCYLVLRS 248 Query: 261 VRTMPVRMAQHARHALEVCEFLQNRPEVVRLYHPAWPADPGHALWQRDCSGSNGMLAVQL 320 + +MPVR+A H R A EV E+L RPEVV++ HPA P PGH W+RD SG+ G+ ++ L Sbjct: 249 LPSMPVRLAAHDRAAREVAEWLTQRPEVVKVLHPALPDCPGHDFWRRDFSGATGLFSIVL 308 Query: 321 GLSPQAAR--DFVNALTLFGIGFSWGGFESL-----VQLVTPGELARHQYWQGGSDALVR 373 A+ FV AL LF IG+SWGG SL VQ + P W+ + LVR Sbjct: 309 HARYTRAQVDAFVEALRLFAIGWSWGGAHSLALPYHVQTMRPQGSWPPVGWENTGE-LVR 367 Query: 374 LHIGLESPADLIADLAQALD 393 L+IGLE DLIADL A++ Sbjct: 368 LYIGLEDTRDLIADLRGAME 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: 439 Number of extensions: 14 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