Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate 3608924 Dshi_2314 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__Dino:3608924 Length = 345 Score = 206 bits (523), Expect = 1e-57 Identities = 136/361 (37%), Positives = 192/361 (53%), Gaps = 28/361 (7%) Query: 1 MRIAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQ 60 M + ++E IG TPL+RLN+ + K E+LNPG S KDR A+ +I A A G Sbjct: 1 MHSYRDLAEAIGHTPLIRLNAASEATGCEILGKAEFLNPGQSVKDRAALYIIRDAVARGT 60 Query: 61 LKPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAV 120 LKPGGTIVE T+GNTG+GLALV G+K V V P+ SE+K+++L GA++V P A Sbjct: 61 LKPGGTIVEGTAGNTGIGLALVGASMGFKTVIVIPETQSEEKKDMLRLAGADLVQVP-AA 119 Query: 121 PPHDPASYYSVSDRLVRDI-----DGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTH 175 P +P +Y S+RL + + GA +Q+ N +H TTGPEIW T GKV Sbjct: 120 PYRNPNNYVRYSERLAKRLAETEPHGAIWANQFDNVANRQAHVETTGPEIWDQTGGKVDG 179 Query: 176 FVAGIGTGGTITGAGRYLKEVSGGRVRIVGADPEGSV----YSGG---AGRPYLVEGVGE 228 F+ G+GGT+ G G L+ V++ ADP+G+ Y+ G + + EG+G+ Sbjct: 180 FICAAGSGGTVAGVGLALQPKG---VKVGLADPDGAALYNFYTQGELKSEGSSISEGIGQ 236 Query: 229 DFWPAAYDPSVPDEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDA 288 A + PD V DS++ + L R E + +GGS G+ + A+++A GP Sbjct: 237 GRITANLEGFTPDFACNVPDSEALPIVFDLLRHEGICLGGSSGINIAGAIRMARHMGPGH 296 Query: 289 LIVVLLPDGGRGYMSKIFNDAWMSSYGFLRSRLDGSTEQSTVGDVLRRKSGALPALVHTH 348 IV +L D G Y SK+FN FLRS+ V D L +LPA+ Sbjct: 297 TIVTILCDYGTRYQSKLFNP------DFLRSK------DLPVPDWLDANPRSLPAVFEEV 344 Query: 349 P 349 P Sbjct: 345 P 345 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: 546 Number of extensions: 41 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: 464 Length of database: 345 Length adjustment: 31 Effective length of query: 433 Effective length of database: 314 Effective search space: 135962 Effective search space used: 135962 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