Align Phosphoserine phosphatase RsbU; EC 3.1.3.3; Sigma factor SigB regulation protein RsbU (uncharacterized)
to candidate WP_010529414.1 ON01_RS02365 PP2C family protein-serine/threonine phosphatase
Query= curated2:P40399 (335 letters) >NCBI__GCF_000224785.1:WP_010529414.1 Length = 336 Score = 368 bits (945), Expect = e-106 Identities = 179/326 (54%), Positives = 247/326 (75%), Gaps = 1/326 (0%) Query: 11 YHQLLSRYIAELTETSLYQAQKFSRKTIEHQIPPEEIISIHRKVLKELYPSLPEDVFHSL 70 Y LL YI E SLY A++ S+ I+ +PPEEII++H + + ELYP P+ S+ Sbjct: 11 YRNLLKHYIQIRDEQSLYGAEQLSKAFIKDNVPPEEIINLHIRAMAELYPDSPDHFQDSM 70 Query: 71 DFLIEVMIGYGMAYQEHQTLRGIQQEIKSEIEIAANVQQTLLGTKVPQEEALDIGAISVP 130 +FL+EVMI YG+A+QE+++LR Q E+KSEI +AAN+Q TLL T P+ + LDIG +SVP Sbjct: 71 NFLLEVMISYGIAHQEYRSLREEQSELKSEIAVAANMQDTLLTTTKPEVDGLDIGVVSVP 130 Query: 131 AKQMSGDYYHFVK-DKESINIAIADVIGKGIPAALCMSMIKYAMDSLPETGIHPSQVLKN 189 A QMSGDYYHF+K + +S+ IA+ADVIGKGIPAALCMSMIKY+MDSLPE + P +LKN Sbjct: 131 AHQMSGDYYHFLKGEDDSLGIAVADVIGKGIPAALCMSMIKYSMDSLPEATMSPKTILKN 190 Query: 190 LNRVVEQNVDASMFITMFYANYNMDKHQFTYASAGHEPGFYYSQKDNTFYDLEAKGLVLG 249 LNRVVE+NVD+SMFITMFYA + +++ YASAGHEPGF+Y TF +++AKGLVLG Sbjct: 191 LNRVVERNVDSSMFITMFYAQFLPYENKLWYASAGHEPGFHYDAATKTFEEIKAKGLVLG 250 Query: 250 ISQDYDYKQFDQHLEKGDMIVLFSDGVTECRTENGFLERPDLQKLIEEHMCSSAQEMVKN 309 ++ D DY+++++ ++KGDM++L +DGVTECR + F+E ++ +I+++ AQEMV Sbjct: 251 VTPDTDYREYERTIDKGDMVILLTDGVTECRQGDRFIETDEVLGVIKQYADLPAQEMVNK 310 Query: 310 IYDSLLKLQDFQLHDDFTLIVLRRKV 335 +Y ++Q+FQL DDFTLIVLR++V Sbjct: 311 VYKHFERMQNFQLRDDFTLIVLRKEV 336 Lambda K H 0.320 0.136 0.385 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: 395 Number of extensions: 11 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: 335 Length of database: 336 Length adjustment: 28 Effective length of query: 307 Effective length of database: 308 Effective search space: 94556 Effective search space used: 94556 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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