The "Organism Name or Classfication or NCBI_TaxID" field allows you to specify terms to limit the search to a range of organisms or to a specific organism (species). A UniProtKB entry will only be returned, if all the given terms appear in either the OS or OC or OX lines of that entry. If in doubt, please consult the UniProtKB list of species. Try to be specific enough, in particular be aware that if you enter "rat", all taxonomical terms containing the substring "rat" will be searched, including "vertebRATa". Entering "rattus" or even "rattus norvegicus" (or even better its TaxID '10116') narrows down your search and probably corresponds better to what you are trying to do.
Scan in UniProtKB/Swiss-Prot can be restricted by the use of a keyword. This should be a keyword in the UniProtKB/Swiss-Prot KW lines. If in doubt, consult the UniProtKB list of keywords.
For example, entering the following values:
pI min = 5.15 pI max = 5.65 Mw = 35000 Mw range = 20% OS/OC/OX = Viridiplantae Keyword = chloroplastwill return all UniProtKB/Swiss-Prot entries for plant chloroplast proteins, with 5.15 <= pI <= 5.65 and 28000 <= Mw <= 42000.
When searching in UniProtKB/Swiss-Prot, TagIdent removes signal sequences and/or propeptides (as documented in the UniProtKB/Swiss-Prot feature table (FT lines)) before computing pI and Mw for each of the resulting chains.
The annotation in UniProtKB/TrEMBL is done automatically; it is incomplete and not always correct. Thus information on UniProtKB/TrEMBL FT lines is not used to process UniProtKB/TrEMBL proteins into mature chains or peptides (i.e. pI and Mw are always computed for the whole sequence), and the use of a keyword is not allowed for searches in UniProtKB/TrEMBL.