ExUniProt-answers

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Answers to "Exercise: Protein databases"

The numbers are found using UniProt on Feb 14, 2014

Simple text mining

QUESTION 1:

  1. How many hits do you find?
    1913
  2. How many hits are from Swiss-Prot? (tip: Click on "Show only reviewed")
    1020
  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 (among the first ten hits).

QUESTION 2: How many hits are now left (still only in Swiss-Prot)?
746

QUESTION 3: How many hits are now left (still only in Swiss-Prot)?
59

QUESTION 4: How many hits are now left?
30

QUESTION 5:

  1. How did you do this?
    by adding NOT name:receptor to the query box.
  2. How many hits are now left?
    20

The content of Swiss-Prot

QUESTION 6:

  1. How many references are there?
    35
  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 7:

  1. Where do you find insulin?
    It is secreted from the cell (this is indicated in Subcellular location under General annotation (Comments) and Cellular component under Ontologies).
  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 8: How long is the signal peptide and the propeptide, respectively?
24 and 31 amino acids.

QUESTION 9: Which positions are in β-sheet conformation in insulin?
Positions 26-29, 48-50, 74-76, and 98-101.

Note: As some of you may have noticed, positions 74-76 are within the propeptide and cannot participate in a beta-sheet in mature insulin. Insulin in its biologically active state is a homodimer (where each subunit consists of an A- and a B-chain), and the beta-sheet is formed between the two subunits, with positions 48-50 from each B-chain forming the strands.

Other databases linked from Swiss-Prot

No questions asked here.

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QUESTION 10: How many proteins did you find, and what was the search string (the text in the Query box)?
79605
annotation:(type:location "secreted")

QUESTION 11: How many proteins do you find now, and what has the search string changed into?
14698
annotation:(type:location "secreted" confidence:experimental)

QUESTION 12: How many proteins do you find now, and what is the search string?
1088
annotation:(type:location "secreted" confidence:experimental) AND organism:"Human [9606]"

QUESTION 13 a: How many proteins are there in UniProt from Neisseria gonorrhoeae with the default TaxID [485]?
1640

QUESTION 13 b: How many proteins are there in UniProt from Neisseria gonorrhoeae in total (all strains and subspecies)?
32316 (almost 20 times as many!)

QUESTION 13 c: What does the search string look like now?
taxonomy:485 or taxonomy:"Neisseria gonorrhoeae [485]", depending on where you look.

QUESTION 14: How many proteins of maximum length 10 do you find?
17124
length:[1 TO 10]

QUESTION 15: How many proteins are now left?
1290
length:[1 TO 10] AND existence:"evidence at protein level"

QUESTION 16: How many proteins are now left?
829
length:[1 TO 10] AND existence:"evidence at protein level" AND fragment:no

QUESTION 17: How many human non-fragment proteins of maximum length 10 do you find in UniProt?
5
length:[1 TO 10] AND existence:"evidence at protein level" AND fragment:no AND organism:"Human [9606]"

QUESTION 18: Here they are in FASTA format:

>sp|P01358|GAJU_HUMAN Gastric juice peptide 1 OS=Homo sapiens PE=1 SV=1
LAAGKVEDSD
>sp|P02728|GLEM_HUMAN Erythrocyte membrane glycopeptide OS=Homo sapiens PE=1 SV=1
CEGHSHDHGA
>sp|P02729|GLUR_HUMAN Urine glycopeptide OS=Homo sapiens PE=1 SV=1
CEHSHDGA
>sp|P22103|PNEU_HUMAN Pneumadin OS=Homo sapiens PE=1 SV=1
AGEPKLDAGV
>sp|P01858|TUFT_HUMAN Phagocytosis-stimulating peptide OS=Homo sapiens PE=1 SV=1
TKPR
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