Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate GFF1601 Psest_1638 cysteine synthase B
Query= SwissProt::P9WP51 (464 letters) >FitnessBrowser__psRCH2:GFF1601 Length = 300 Score = 198 bits (504), Expect = 2e-55 Identities = 114/299 (38%), Positives = 173/299 (57%), Gaps = 16/299 (5%) Query: 7 ISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGT 66 I++ IG TPLVRL + + T+ K+E NP GS KDR A+ MI AE G ++PG T Sbjct: 8 IADCIGNTPLVRLQRMPGKTSNTILVKLEGNNPAGSVKDRPALSMINRAELRGDIQPGDT 67 Query: 67 IVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPA 126 ++E TSGNTG+ LA+ A +GY+ + + PD + +++ + AYGAE+++ + Sbjct: 68 LIEATSGNTGIALAMAAAIKGYRMILIMPDNSTAERKAAMTAYGAELILV-----SKEEG 122 Query: 127 SYYSVSDRLVRDIDGAWKP-DQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGT 185 + L +G K DQ+AN + P +HY +TGPE+W T G +THF++ +GT GT Sbjct: 123 MEGARDLALKMQAEGRGKVLDQFANGDNPEAHYNSTGPELWRQTHGSITHFISSMGTTGT 182 Query: 186 ITGAGRYLKEVSGGRVRIVGADP-EGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEII 244 I G RYLKE V+IVG P EG+ G P +++ P Y D ++ Sbjct: 183 IMGVSRYLKE-QNPAVQIVGLQPMEGAAIPGIRRWP-------QEYLPKIYQAERVDRVV 234 Query: 245 AVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMS 303 +S +++ + RRLAREE + G S G AV AAL++++E +A+IV ++ D G Y+S Sbjct: 235 DMSQAEAEQVMRRLAREEGIFCGVSSGGAVAAALRLSQEV-ENAVIVAIICDRGDRYLS 292 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: 363 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 464 Length of database: 300 Length adjustment: 30 Effective length of query: 434 Effective length of database: 270 Effective search space: 117180 Effective search space used: 117180 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