ExUniProt-answers

The numbers are found using UniProt 2025_03 on Sep 16, 2025

Simple text mining

QUESTION 1.1:

1. How many hits do you find?
   35,870
2. How many of these hits are from Swiss-Prot?
   1,774
3. Can you identify the correct hit (i.e. see which one is actually human insulin and not something else)?
   It's P01308 / INS_HUMAN (not necessarily the top hit, but still on the first page).

QUESTION 1.2: How many hits are now left? How many of these are from Swiss-Prot?
2,375 and 1,157

QUESTION 1.3: How many hits are now left? How many of these are from Swiss-Prot?
217 and 60, search string: (organism_id:9606) AND (protein_name:insulin)

QUESTION 1.4: How many hits are now left? How many of these are from Swiss-Prot?
68 and 25, search string: (organism_id:9606) AND (protein_name:insulin) NOT (protein_name:insulin-like)

QUESTION 1.5:

1. How did you do this?
   by adding NOT (protein_name:receptor) to the query box.
2. How many hits are now left? How many of these are from Swiss-Prot?
   49 and 16

The contents of UniProt

QUESTION 2.1:

1. How many references are there in the insulin entry?
   37
2. Why do you think insulin is such a highly investigated protein?
   Because it is linked to a common and serious disease (diabetes) and used as a drug.

QUESTION 2.2:

1. Where do you find insulin?
   It is secreted from the cell (this is written just below the section heading. Under GO - Cellular component you can find additional locations mentioned, such as endoplasmic reticulum lumen, but these are temporary stages on the way to secretion).
2. Why do you think is it found there?
   Because it is a hormone - it has to travel through the bloodstream to influence other cells.

QUESTION 2.3: How long is the signal peptide and the propeptide, respectively?
24 and 31 amino acids.

Other databases linked from UniProt

QUESTION 2.4: How many mRNA sequences can you find links to, and what are their identifiers?
There are four mRNA sequences linked, and they are called: X70508, AY899304, BT006808, and BC005255.

QUESTION 2.5: What is the PDB Identifier of that structure?
The first structure to contain only one A and one B chain is 9R4E, number 3 in the list. Screenshot is here:

QUESTION 2.6: What is the InterPro identifier of the family that is just called "Insulin" and nothing else?
IPR004825.

Text format

QUESTION 2.7: Find the two feature table lines that describe the signal peptide and copy them to your answer.

FT   SIGNAL          1..24
FT                   /evidence="ECO:0000269|PubMed:14426955"

Advanced search

QUESTION 3.1: How many proteins did you find, and what was the search string (the text in the search field)?
12,497,853, of these 45,490 from Swiss-Prot
(ft_signal:*)

QUESTION 3.2: How many proteins do you find now, and what has the search string changed into?
3,922, they are all from Swiss-Prot
(ft_signal_exp:*)
Note that the "experimental" evidence is only found in Swiss-Prot entries, not in TrEMBL!

QUESTION 3.3: How many proteins do you find now, and what is the search string?
742
(ft_signal_exp:*) AND (organism_id:9606)

QUESTION 3.4: How many proteins are there in UniProt from Bacillus subtilis with the default TaxID [1423]?
903 results, of these only 63 from Swiss-Prot
(organism_id:1423)

QUESTION 3.5: How many proteins are there in UniProt from Bacillus subtilis in total (all strains and subspecies)?
5,341, of these 4,280 from Swiss-Prot
(taxonomy_id:1423)

QUESTION 3.6: How many proteins of maximum length 10 do you find?
9,009
(length:[1 TO 10])

QUESTION 3.7: How many proteins are now left?
1,324
(length:[1 TO 10]) AND (existence:1)

QUESTION 3.8: How many proteins are now left?
889
(length:[1 TO 10]) AND (existence:1) AND (fragment:false)

QUESTION 3.9: How many human non-fragment proteins of maximum length 10 do you find in UniProt?
6
(length:[1 TO 10]) AND (existence:1) AND (fragment:false) AND (organism_id:9606)

QUESTION 3.10:

Here they are in FASTA format:

>sp|P0DPR3|TRDD1_HUMAN T cell receptor delta diversity 1 OS=Homo sapiens OX=9606 GN=TRDD1 PE=1 SV=1
EI
>sp|P01858|TUFT_HUMAN Phagocytosis-stimulating peptide OS=Homo sapiens OX=9606 PE=1 SV=1
TKPR
>sp|P02729|GLUR_HUMAN Urine glycopeptide OS=Homo sapiens OX=9606 PE=1 SV=1
CEHSHDGA
>sp|P01358|GAJU_HUMAN Gastric juice peptide 1 OS=Homo sapiens OX=9606 PE=1 SV=1
LAAGKVEDSD
>sp|P02728|GLEM_HUMAN Erythrocyte membrane glycopeptide OS=Homo sapiens OX=9606 PE=1 SV=1
CEGHSHDHGA
>sp|P22103|PNEU_HUMAN Pneumadin OS=Homo sapiens OX=9606 PE=1 SV=1
AGEPKLDAGV

On your own

QUESTION 4.1: (taxonomy_id:562), 762,443 hits.

QUESTION 4.2: (taxonomy_id:83334), 18,197 hits.

QUESTION 4.3: (protein_name:insulin) AND (gene:ins) NOT (protein_name:insulin-like) NOT (protein_name:"insulin related"), 602 hits
(This is a question that does not have one single correct answer)

QUESTION 4.4: (protein_name:"alpha globin") AND (taxonomy_id:9845) NOT (protein_name:"transcription factor"), 17 hits.

QUESTION 4.5: (protein_name:"alpha-* globin") AND (taxonomy_id:8932), 2 hits.