Explore features of a protein of interest

ProteomeScoutAPI allows for easy access of features associated with any protein of interest. Let’s say, for example, we wanted to better understand the PTMs, domains, and other features associated with the tyrosine kinase SRC (UniProt ID = P12931).

First, initialize the API:

import proteomeScoutAPI
api = proteomeScoutAPI.ProteomeScoutAPI()

Let’s first get an idea of the structure of SRC. What domains are present in the protein, focusing on interpro definitions?

api.get_domains('P12931', domain_type = 'interpro')

[('SH3_domain', '84', '145', 'IPR001452'),
 ('SH2', '149', '248', 'IPR000980'),
 ('Prot_kinase_dom', '270', '523', 'IPR000719')]

Here, we can see there are three domains in SRC, provided as a list of tuples. Each tuple contains the domain name, start position in the protein, end position in the protein, and interpro ID.

We can easily convert this list to a dataframe if you prefer:

import pandas as pd
domains = api.get_domains('P12931', domain_type = 'interpro')
domains = pd.DataFrame(domains, columns = ['Domain_Name', 'Start', 'End', 'InterPro_ID'])
domains

	Domain_Name	Start	End	InterPro_ID
0	SH3_domain	84	145	IPR001452
1	SH2	149	248	IPR000980
2	Prot_kinase_dom	270	523	IPR000719

If want to also get the structure, PTMs, or other details about the protein, we can repeat the same as above, but using api.get_structures(), api.get_macro_molecular(), or api.get_PTMs().

In some cases, you might also want to get PTMs AND information about where each PTM is located in the protein. We have provided an additional function for quickly getting this info (api.get_annotated_ptms()). This will output a dataframe containing the standard information about the PTM (position, residue, and type of modification), but will also indicate whether the PTM is associated with a specific domain, structure, or macromolecular instance.

api.get_annotated_PTMs('P12931')

	Position	Residue	Modification_Type	evidence	Domain_Names_InterPro	InterPro_IDs	Domain_Names_UniProt	Structures	Macro_Molecular_Structures
0	2	G	N-myristoyl glycine	1395,1575					Disordered
1	12	S	Phosphoserine	1323,1395,1575,1718,1719,1790					Disordered;Basic and acidic residues
2	17	S	Phosphoserine	1886,1323,1395,1575,1718,1723,1790,1803					Disordered;Basic and acidic residues
3	35	S	Phosphoserine	1575,1790,1803					Disordered
4	37	T	Phosphothreonine	1575,1790					Disordered
5	39	S	Phosphoserine	1575,1790					Disordered
6	43	S	Phosphoserine	1790					Disordered
7	51	S	Phosphoserine	1790					Disordered
8	62	K	N6-acetyllysine	1790
9	69	S	Phosphoserine	1323,1575,1718,1723,1790,1803
10	70	S	Phosphoserine	1575,1790
11	72	T	Phosphothreonine	1575,1790
12	74	T	Phosphothreonine	1323,1395,1575,1790,1803
13	75	S	Phosphoserine	1886,1323,1395,1575,1718,1719,1723,1790,1803
14	93	Y	Phosphotyrosine	1790	SH3_domain	IPR001452	SH3	STRAND
15	97	S	Phosphoserine	1323,1395,1575,1790	SH3_domain	IPR001452	SH3
16	104	S	Phosphoserine	1723,1790	SH3_domain	IPR001452	SH3
17	182	T	Phosphothreonine	1790	SH2	IPR000980	SH2	STRAND
18	183	T	Phosphothreonine	1790	SH2	IPR000980	SH2	STRAND
19	187	Y	Phosphotyrosine	1886,1521,1575,1787,1790,1803	SH2	IPR000980	SH2	STRAND
20	216	Y	Phosphotyrosine	1323,1395,1575,1790	SH2	IPR000980	SH2	STRAND
21	246	T	Phosphothreonine	1790	SH2	IPR000980	SH2
22	250	T	Phosphothreonine	1790
23	255	T	Phosphothreonine	1790
24	269	S	Phosphoserine	1790				HELIX
25	304	T	Phosphothreonine	1790	Prot_kinase_dom	IPR000719	Protein kinase	TURN
26	306	S	Phosphoserine	1395,1575,1790	Prot_kinase_dom	IPR000719	Protein kinase
27	338	Y	Phosphotyrosine	1323,1575,1790	Prot_kinase_dom	IPR000719	Protein kinase	STRAND
28	348	S	Phosphoserine	1790	Prot_kinase_dom	IPR000719	Protein kinase	STRAND
29	385	Y	Phosphotyrosine	1790	Prot_kinase_dom	IPR000719	Protein kinase
30	419	Y	Phosphotyrosine	1886,1323,1395,1575,1718,1719,1790,1803	Prot_kinase_dom	IPR000719	Protein kinase	HELIX
31	420	T	Phosphothreonine	1575,1790	Prot_kinase_dom	IPR000719	Protein kinase	HELIX
32	430	K	Ubiquitination	1790	Prot_kinase_dom	IPR000719	Protein kinase	HELIX
33	439	Y	Phosphotyrosine	1323,1575,1790,1803	Prot_kinase_dom	IPR000719	Protein kinase	HELIX
34	511	T	Phosphothreonine	1575,1803	Prot_kinase_dom	IPR000719	Protein kinase
35	522	Y	Phosphotyrosine	1575,1790,1803	Prot_kinase_dom	IPR000719	Protein kinase	TURN
36	525	S	Phosphoserine	1575,1790
37	526	T	Phosphothreonine	1790
38	530	Y	Phosphotyrosine	1323,1395,1575,1787,1790,1803,1886