Align Phosphoserine phosphatase RsbU; EC 3.1.3.3; Sigma factor SigB regulation protein RsbU (uncharacterized)
to candidate WP_004513986.1 GMET_RS14120 PAS domain S-box protein
Query= curated2:P40399 (335 letters) >NCBI__GCF_000012925.1:WP_004513986.1 Length = 649 Score = 113 bits (282), Expect = 2e-29 Identities = 69/219 (31%), Positives = 115/219 (52%), Gaps = 9/219 (4%) Query: 77 MIGYGMAYQEHQTLRGIQQE-------IKSEIEIAANVQQTLLGTKVPQEEALDIGAISV 129 ++ + +A +E T R QE + ++E+A +Q LL + P + V Sbjct: 369 VVRHYVAIKEDVTERKRAQEALLENARMSCDMELARQIQGALLPSAPPVVAGVRCAGRWV 428 Query: 130 PAKQMSGDYYHFV-KDKESINIAIADVIGKGIPAALCMSMIKYAMDSLPETGIHPSQVLK 188 PA + GDYY F +D S + IADV G + AAL M+ + + + +G P+ +++ Sbjct: 429 PAAHVGGDYYDFFPRDDGSFDTVIADVSGHSVGAALIMTEARSVIRTQARSGGSPAAIVR 488 Query: 189 NLNR-VVEQNVDASMFITMFYANYNMDKHQFTYASAGHEPGFYYSQKDNTFYDLEAKGLV 247 +LN + E A +F TMFYA+Y TYASAGH P Y + + +L+A GL+ Sbjct: 489 SLNENLYEDLTRAELFTTMFYASYRPTSGILTYASAGHNPPLLYRRAEGRCLELDADGLI 548 Query: 248 LGISQDYDYKQFDQHLEKGDMIVLFSDGVTECRTENGFL 286 LG+ +++ + L GD+++L++DG+TE +G L Sbjct: 549 LGVKPQVTFEEREVRLAPGDILLLYTDGITESDNGSGEL 587 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: 430 Number of extensions: 19 Number of successful extensions: 3 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: 649 Length adjustment: 33 Effective length of query: 302 Effective length of database: 616 Effective search space: 186032 Effective search space used: 186032 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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