Explore features of a protein of interest

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:

[1]:

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?

[2]:

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

[2]:

[('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:

[3]:

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

[3]:
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.

[5]:

api.get_annotated_PTMs('P12931')

[5]:
Position Residue Modification_Type evidence SpY-C Prediction SpY-C Prediction Probability Domain_Names_InterPro InterPro_IDs Domain_Names_UniProt Structures Macro_Molecular_Structures Activation_Loop_Quality In_Activation_Loop Exons Exon_Constitutive In_Exon
0 2 G N-myristoyl glycine 1395,1575,1888 Disordered False ENSE00000661877 0 True
1 6 S Phosphoserine 1888 Disordered False ENSE00000661877 0 True
2 12 S Phosphoserine 1323,1395,1575,1718,1719,1790,1888 Disordered;Basic and acidic residues False ENSE00000661877 0 True
3 17 S Phosphoserine 1323,1395,1575,1718,1723,1790,1803,1886,1888 Disordered;Basic and acidic residues False ENSE00000661877 0 True
4 35 S Phosphoserine 1575,1790,1803,1888 Disordered False ENSE00000661877 0 True
5 37 T Phosphothreonine 1575,1790,1888 Disordered False ENSE00000661877 0 True
6 39 S Phosphoserine 1575,1790,1888 Disordered False ENSE00000661877 0 True
7 43 S Phosphoserine 1790,1888 Disordered False ENSE00000661877 0 True
8 51 S Phosphoserine 1790,1888 Disordered False ENSE00000661877 0 True
9 62 K Acetylation 1888 False ENSE00000661877 0 True
10 69 S Phosphoserine 1323,1575,1718,1723,1790,1803,1888 False ENSE00000661877 0 True
11 70 S Phosphoserine 1575,1790,1888 False ENSE00000661877 0 True
12 72 T Phosphothreonine 1575,1790,1888 False ENSE00000661877 0 True
13 74 T Phosphothreonine 1323,1395,1575,1790,1803,1888 False ENSE00000661877 0 True
14 75 S Phosphoserine 1323,1395,1575,1718,1719,1723,1790,1803,1886,1888 False ENSE00000661877 0 True
15 97 S Phosphoserine 1323,1395,1575,1790,1888 SH3_domain IPR001452 SH3 False ENSE00003544319 0 True
16 101 T Phosphothreonine 1888 SH3_domain IPR001452 SH3 STRAND False ENSE00003544319 0 True
17 104 S Phosphoserine 1723,1790,1888 SH3_domain IPR001452 SH3 False ENSE00003544319 0 True
18 106 K Ubiquitination 1888 SH3_domain IPR001452 SH3 False ENSE00003544319 0 True
19 180 S Phosphoserine 1888 SH2 IPR000980 SH2 False ENSE00003523341 0 True
20 182 T Phosphothreonine 1790,1888 SH2 IPR000980 SH2 STRAND False ENSE00003523341 0 True
21 183 T Phosphothreonine 1790,1888 SH2 IPR000980 SH2 STRAND False ENSE00003523341 0 True
22 184 K Ubiquitination 1888 SH2 IPR000980 SH2 False ENSE00003523341 0 True
23 187 Y Phosphotyrosine 1521,1575,1787,1790,1803,1886,1888 low-confidence 0.4563833554946678 SH2 IPR000980 SH2 STRAND False ENSE00003678936 0 True
24 190 S Phosphoserine 1888 SH2 IPR000980 SH2 STRAND False ENSE00003678936 0 True
25 203 K Acetylation 1888 SH2 IPR000980 SH2 STRAND False ENSE00003678936 0 True
26 212 S Phosphoserine 1888 SH2 IPR000980 SH2 STRAND False ENSE00003678936 0 True
27 216 Y Phosphotyrosine 1323,1395,1575,1790,1888 binder 0.7092145709467987 SH2 IPR000980 SH2 STRAND False ENSE00003678936 0 True
28 218 T Phosphothreonine 1888 SH2 IPR000980 SH2 STRAND False ENSE00003678936 0 True
29 219 S Phosphoserine 1888 SH2 IPR000980 SH2 False ENSE00003678936 0 True
30 252 K Ubiquitination 1888 False ENSE00003516229 0 True
31 255 T Phosphothreonine 1790,1888 False ENSE00003516229 0 True
32 269 S Phosphoserine 1790,1888 HELIX False ENSE00003516229 0 True
33 298 K Ubiquitination 1888 Prot_kinase_dom IPR000719 Protein kinase STRAND False ENSE00003564760 0 True
34 304 T Phosphothreonine 1790,1888 Prot_kinase_dom IPR000719 Protein kinase TURN False ENSE00003564760 0 True
35 306 S Phosphoserine 1395,1575,1790,1888 Prot_kinase_dom IPR000719 Protein kinase False ENSE00003564760 0 True
36 338 Y Phosphotyrosine 1323,1575,1790,1888 binder 0.7244592047569105 Prot_kinase_dom IPR000719 Protein kinase STRAND False ENSE00003564760 0 True
37 348 S Phosphoserine 1790,1888 Prot_kinase_dom IPR000719 Protein kinase STRAND False ENSE00003669255 0 True
38 375 S Phosphoserine 1888 Prot_kinase_dom IPR000719 Protein kinase HELIX False ENSE00003543788 0 True
39 379 Y Phosphotyrosine 1888 binder 0.625708757989302 Prot_kinase_dom IPR000719 Protein kinase HELIX False ENSE00003543788 0 True
40 385 Y Phosphotyrosine 1790,1888 nonbinder 0.0768720113308754 Prot_kinase_dom IPR000719 Protein kinase False ENSE00003543788 0 True
41 404 K Ubiquitination 1888 Prot_kinase_dom IPR000719 Protein kinase STRAND False ENSE00003543788 0 True
42 419 Y Phosphotyrosine 1323,1395,1575,1718,1719,1790,1803,1886,1888 nonbinder 0.1063481666062969 Prot_kinase_dom IPR000719 Protein kinase HELIX HIGH True ENSE00003543788 0 True
43 420 T Phosphothreonine 1575,1790,1888 Prot_kinase_dom IPR000719 Protein kinase HELIX HIGH True ENSE00003543788 0 True
44 426 K Ubiquitination 1888 Prot_kinase_dom IPR000719 Protein kinase TURN HIGH True ENSE00003638193 0 True
45 430 K Ubiquitination 1790,1888 Prot_kinase_dom IPR000719 Protein kinase HELIX HIGH True ENSE00003638193 0 True
46 439 Y Phosphotyrosine 1323,1575,1790,1803,1888 binder 0.6554389457324623 Prot_kinase_dom IPR000719 Protein kinase HELIX False ENSE00003638193 0 True
47 443 T Phosphothreonine 1888 Prot_kinase_dom IPR000719 Protein kinase False ENSE00003638193 0 True
48 511 T Phosphothreonine 1575,1803,1888 Prot_kinase_dom IPR000719 Protein kinase False ENSE00001460955 0 True
49 522 Y Phosphotyrosine 1575,1790,1803,1888 nonbinder 0.0800138914816677 Prot_kinase_dom IPR000719 Protein kinase TURN False ENSE00001460955 0 True
50 524 T Phosphothreonine 1888 False ENSE00001460955 0 True
51 525 S Phosphoserine 1575,1790,1888 False ENSE00001460955 0 True
52 526 T Phosphothreonine 1790,1888 False ENSE00001460955 0 True
53 530 Y Phosphotyrosine 1323,1395,1575,1787,1790,1803,1886,1888 nonbinder 0.0116835110116847 False ENSE00001460955 0 True