Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate 202695 SO3598 cysteine synthase B (NCBI ptt file)
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__MR1:202695 Length = 288 Score = 187 bits (474), Expect = 5e-52 Identities = 113/299 (37%), Positives = 170/299 (56%), Gaps = 20/299 (6%) Query: 7 ISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGT 66 I IG TPLVRL + G+ TV K+E NP GS KDR A+ MI AE ++ PG T Sbjct: 3 IEACIGQTPLVRLQRL-DCGSSTVLLKLEGNNPAGSVKDRAALNMINQAELRQEIAPGDT 61 Query: 67 IVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPA 126 ++E TSGNTG+ LA+ A +GYK + + P ++++++ + AYGAE+++ D A Sbjct: 62 LIEATSGNTGIALAMAAAIKGYKMILIMPSNSTQERKDAMQAYGAELLLVDNMEAARDLA 121 Query: 127 SYYSVSDRLVRDIDGAWKP-DQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGT 185 L +G K DQ+ N + +H++TTGPEIW ++GK+THFV+ +GT GT Sbjct: 122 --------LALQAEGKGKVLDQFNNQDNANAHFLTTGPEIWQQSQGKITHFVSSMGTTGT 173 Query: 186 ITGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEII 244 I G +YLK + IVG P +GS G P +++ P +D + D ++ Sbjct: 174 IMGVSKYLKS-RNPDITIVGLQPADGSSIPGIRRWP-------QEYLPGIFDAARVDLMM 225 Query: 245 AVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMS 303 + + D+ M R LAREE + G S G AV AAL++A + P +++V ++ D G Y+S Sbjct: 226 DIEEQDAKAMARALAREEGICAGVSSGGAVYAALELARQY-PGSVVVAIVCDRGDRYLS 283 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: 328 Number of extensions: 17 Number of successful extensions: 2 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: 288 Length adjustment: 30 Effective length of query: 434 Effective length of database: 258 Effective search space: 111972 Effective search space used: 111972 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: 49 (23.5 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