Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized)
to candidate PP_1654 PP_1654 cysteine synthase B
Query= metacyc::MONOMER-20568 (299 letters) >FitnessBrowser__Putida:PP_1654 Length = 299 Score = 264 bits (675), Expect = 2e-75 Identities = 133/295 (45%), Positives = 197/295 (66%), Gaps = 2/295 (0%) Query: 3 YDNILETIGNTPLVRINHLNPNPKVQMYAKLEGFNPTGSVKDRIALKMIEQAEAEGKLHP 62 Y I + +GNTPLVR+ + + KLEG NP GSVKDR AL MI +AE G++ P Sbjct: 5 YPTIADCVGNTPLVRLQRIAGETSNTLLLKLEGNNPAGSVKDRPALSMIARAELRGQIKP 64 Query: 63 GSTIIEATSGNTGIGLAMIGRVKGYNVIIVMSEGVSIERRKMIKAFGAEIILTDKKLGTD 122 G T+IEATSGNTGI LAM +KGY +I++M + + ER+ + A+GAE+IL K+ G + Sbjct: 65 GDTLIEATSGNTGIALAMAAAIKGYKMILIMPDNSTAERKAAMTAYGAELILVTKEEGME 124 Query: 123 GAIRKVAELVKENPGKYFNPNQFSNEYNKIAHYKTTAEEIWAQTKGTVTHFVAAVGTSGT 182 GA R +AE ++ G+ +QF+N N IAHY +T EIW QT+GT+THFV+++GT+GT Sbjct: 125 GA-RDLAEKLQAE-GRGLVLDQFANGDNPIAHYNSTGPEIWQQTQGTITHFVSSMGTTGT 182 Query: 183 LMGVGKNLREKNPEIKIIEAQPTKGHYIQGLKSMEEAIVPAIYQADKIDEHILIESEEAF 242 +MG + L+E+NP ++II QP +G I G++ E +P I+ A ++D + + +EA Sbjct: 183 IMGCSQYLKEQNPAVQIIGLQPMEGSAIPGIRRWPEEYLPKIFDATRVDRVVDMSQQEAE 242 Query: 243 AKAREIVAQEGIFIGMSSGAAMLAAQKLAEKIDSGVIVVLFADRGEKYLSTKLFD 297 R + +EGIF G+SSG A+ A +L+ ++++ V+V + DRG++YLST LFD Sbjct: 243 DTTRRLAREEGIFCGVSSGGAVAAMLRLSREVENAVMVAIICDRGDRYLSTGLFD 297 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: 299 Number of extensions: 18 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: 299 Length adjustment: 27 Effective length of query: 272 Effective length of database: 272 Effective search space: 73984 Effective search space used: 73984 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