Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate GFF1601 Psest_1638 cysteine synthase B
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__psRCH2:GFF1601 Length = 300 Score = 266 bits (679), Expect = 6e-76 Identities = 130/296 (43%), Positives = 196/296 (66%), Gaps = 2/296 (0%) Query: 3 YDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHP 62 Y I + IGNTPLVR+ + + KLEG NP GSVKDR AL MI +AE G + P Sbjct: 5 YPTIADCIGNTPLVRLQRMPGKTSNTILVKLEGNNPAGSVKDRPALSMINRAELRGDIQP 64 Query: 63 GSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTD 122 G T+IEATSGNTGI LAM +KGY +I++M + + ER+ + A+GAE+IL K+ G + Sbjct: 65 GDTLIEATSGNTGIALAMAAAIKGYRMILIMPDNSTAERKAAMTAYGAELILVSKEEGME 124 Query: 123 GAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGT 182 GA ++ E GK + QF+N N AHY +T E+W QT G++THF++++GT+GT Sbjct: 125 GARDLALKMQAEGRGKVLD--QFANGDNPEAHYNSTGPELWRQTHGSITHFISSMGTTGT 182 Query: 183 LMGVGKNLREKNPEIKIIEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAF 242 +MGV + L+E+NP ++I+ QP +G I G++ + +P IYQA+++D + + EA Sbjct: 183 IMGVSRYLKEQNPAVQIVGLQPMEGAAIPGIRRWPQEYLPKIYQAERVDRVVDMSQAEAE 242 Query: 243 AKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLFADRGEKYLSTKLFDT 298 R + +EGIF G+SSG A+ AA +L++++++ VIV + DRG++YLST ++D+ Sbjct: 243 QVMRRLAREEGIFCGVSSGGAVAAALRLSQEVENAVIVAIICDRGDRYLSTGVYDS 298 Lambda K H 0.315 0.133 0.367 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: 311 Number of extensions: 22 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: 299 Length of database: 300 Length adjustment: 27 Effective length of query: 272 Effective length of database: 273 Effective search space: 74256 Effective search space used: 74256 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: 42 (22.0 bits) S2: 48 (23.1 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