Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate RR42_RS11250 RR42_RS11250 cysteine synthase
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__Cup4G11:RR42_RS11250 Length = 336 Score = 231 bits (590), Expect = 2e-65 Identities = 136/313 (43%), Positives = 177/313 (56%), Gaps = 9/313 (2%) Query: 11 IGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGTIVEP 70 IG TPL+RL + + + K E+LNPGGS KDR A+ +I AE G LKPGGT+VE Sbjct: 11 IGHTPLIRLAGLSEETGCEILGKAEFLNPGGSVKDRAALYIIRDAERRGALKPGGTVVEG 70 Query: 71 TSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPASYYS 130 T+GNTG+GLA + RGY+C+ V PD S +K + L GAEV P A P DP +Y Sbjct: 71 TAGNTGIGLAHLCAARGYRCIVVIPDTQSPEKMDRLRLLGAEVRPVP-AAPYADPNNYQK 129 Query: 131 VSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGTITGAG 190 V+ RL ++ + A +Q+ N +HY TTGPEIW DT GK+ FV GTGGT+ G Sbjct: 130 VAGRLAQETENAIWANQFDNLANRQAHYETTGPEIWHDTAGKIDAFVCATGTGGTLAGVA 189 Query: 191 RYLKEVS-GGRVRIVGADPEGS-------VYSGGAGRPYLVEGVGEDFWPAAYDPSVPDE 242 R+LKE VRIV ADP GS + A + EG+G A + D+ Sbjct: 190 RFLKEKERNPPVRIVLADPHGSGLYHFVKHHEVKAKGNSITEGIGSSRVTANLADTPIDD 249 Query: 243 IIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYM 302 + + D DM RL REE + VGGS G+ V AA +A E GP IV LL D G Y Sbjct: 250 AVRIDDQACVDMVYRLLREEGLWVGGSSGINVAAAAWLAREMGPGHTIVTLLCDRGDLYA 309 Query: 303 SKIFNDAWMSSYG 315 ++FN W+++ G Sbjct: 310 GRLFNADWLAAKG 322 Lambda K H 0.316 0.135 0.398 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: 486 Number of extensions: 35 Number of successful extensions: 3 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: 464 Length of database: 336 Length adjustment: 31 Effective length of query: 433 Effective length of database: 305 Effective search space: 132065 Effective search space used: 132065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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