On linux just type:

sort <(cat list.txt) <(grep '>' uniprot.fa | cut -c5-10) | uniq -d

to get a list of UniProt IDs that are present in your fasta file.

If you want to list IDs that don't appear among fasta records, just change uniq -d to uniq -u.

extract the IDs from the fasta header, sort both files, use comm

Python script below. Save it in a file like myscript.py

from sets import Set
import sys

# parameters: uniprotfile fastafile

uniprotfile = open(sys.argv[1])
fastafile = open(sys.argv[2])


A = Set([])

for line in uniprotfile:
    line = line.strip()
    A.add(line)

B = Set([])
for line in fastafile:
    if line.startswith('>'):
        line = line[1:].strip()
        B.add(line)


C = A.intersection(B) #names that are in both FASTA and UniProt list
print "Present:"
for el in C:
    print el

print
print "Not present:"
D = A.difference(B) #names not found in fasta
for el in D:
    print el

Next, run the script in this way: python myscript uniprot.txt fasta.fa