Extract information

From text

The human proteome is downloaded from UniProt - Reviewed Swiss-Prot. As of Jule 27th, 2024, it has compiled 20435 expert-reviewed human genes that encode proteins. As UniProt sequences in Text format contains information about the sequences, structures,and functions of proteins, users can extract as comprehensive information as possible from the Text file.

The following examples show how we use pypropel to achieve this functionality.

import pypropel as pp

df = pp.uniprot.from_text(
    text_fpn=to('data/uniprot/text/uniprotkb_Human_AND_reviewed_true_AND_m_2023_11_29.txt'),
    sv_json_fpn=to('data/uniprot/text/human.json'),
    sv_df_fpn=to('data/uniprot/text/human.txt'),
)

The output of the pp.uniprot.from_text function.

ID  AC  DE  GN  Ensembl_G_id    Ensembl_T_id    SQ  tms_nums    binding_nums    binding_sites   pdb_nums    pdb_ids pdb_chains  pdb_rezs
CP2D7_HUMAN A0A087X1C5  RecName: Full=Putative cytochrome P450 2D7 {ECO:0000305}; EC=1.14.14.1 {ECO:0000269|PubMed:15051713};   CYP2D7  NaN     MGLEALVPLAMIVAIFLLLVDLMHRHQRWAARYPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREAMVTRGEDTADRPPAPIYQVLGFGPRSQGVILSRYGPAWREQRRFSVSTLRNLGLGKKSLEQWVTEEAACLCAAFADQAGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLPHIPALAGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAKKEKAKGSPESSFNDENLRIVVGNLFLAGMVTTSTTLAWGLLLMILHLDVQRGRRVSPGCPIVGTHVCPVRVQQEIDDVIGQVRRPEMGDQAHMPCTTAVIHEVQHFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWKKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVAAGQPRPSHSRVVSFLVTPSPYELCAVPR 2   1   461 0           
PIOS1_HUMAN A0A0B4J2F0  RecName: Full=Protein PIGBOS1 {ECO:0000305}; AltName: Full=PIGB opposite strand protein 1 {ECO:0000312|HGNC:HGNC:50696};    PIGBOS1 ENSG00000225973 ENST00000436697.3;ENST00000567948.1 MFRRLTFAQLLFATVLGIAGGVYIFQPVFEQYAKDQKELKEKMQLVQESEEKKS  1   0       0   
E2F8_HUMAN  A0AVK6  RecName: Full=Transcription factor E2F8; Short=E2F-8;   E2F8    ENSG00000129173 ENST00000250024.9;ENST00000527884.5;ENST00000620009.4   MENEKENLFCEPHKRGLMKTPLKESTTANIVLAEIQPDFGPLTTPTKPKEGSQGEPWTPTANLKMLISAVSPEIRNRDQKRGLFDNRSGLPEAKDCIHEHLSGDEFEKSQPSRKEKSLGLLCHKFLARYPNYPNPAVNNDICLDEVAEELNVERRRIYDIVNVLESLHMVSRLAKNRYTWHGRHNLNKTLGTLKSIGEENKYAEQIMMIKKKEYEQEFDFIKSYSIEDHIIKSNTGPNGHPDMCFVELPGVEFRAASVNSRKDKSLRVMSQKFVMLFLVSTPQIVSLEVAAKILIGEDHVEDLDKSKFKTKIRRLYDIANVLSSLDLIKKVHVTEERGRKPAFKWTGPEISPNTSGSSPVIHFTPSDLEVRRSSKENCAKNLFSTRGKPNFTRHPSLIKLVKSIESDRRKINSAPSSPIKTNKAESSQNSAPFPSKMAQLAAICKMQLEEQSSESRQKVKVQLARSGPCKPVAPLDPPVNAEMELTAPSLIQPLGMVPLIPSPLSSAVPLILPQAPSGPSYAIYLQPTQAHQSVTPPQGLSPTVCTTHSSKATGSKDSTDATTEKAANDTSKASASTRPGSLLPAPERQGAKSRTREPAGERGSKRASMLEDSGSKKKFKEDLKGLENVSATLFPSGYLIPLTQCSSLGAESILSGKENSSALSPNHRIYSSPIAGVIPVTSSELTAVNFPSFHVTPLKLMVSPTSVAAVPVGNSPALASSHPVPIQNPSSAIVNFTLQHLGLISPNVQLSASPGSGIVPVSPRIESVNVAPENAGTQQGRATNYDSPVPGQSQPNGQSVAVTGAQQPVPVTPKGSQLVAESFFRTPGGPTKPTSSSCMDFEGANKTSLGTLFVPQRKLEVSTEDVH 0   0       1   4YO2    A=110-341   3.07
...

The information extracted is shown as follows.

{
    'ID': Uniprot ,
    'AC': Uniprot accession code,
    'DE': Description,
    'GN': gene names,
    'Ensembl_G_id': ensembl gene ID,
    'Ensembl_T_id': ensembl transcript ID,
    'SQ': sequence,
    'tms_nums': number of transmembrane segments,
    'binding_nums': numbers of binding sites,
    'binding_sites': PDB IDs of binding sites,
    'pdb_nums': number of PDB structures,
    'pdb_ids': IDS of PDB structures,
    'pdb_chains': IDs of PDB chains,
    'pdb_rezs': resolutions of PDB structures,
}

This function will also output a file in json format. It gives specific PDB IDs of the extracted transmembrane segments in tmh_lower and tmh_upper.

{"CP2D7_HUMAN": {"pac": "A0A087X1C5", "gn": "CYP2D7", "ensembl_id": "NaN", "binding_num": 1, "pdb_num": 0, "cyto_lower": [24], "cyto_upper": [301], "extra_lower": [1, 323], "extra_upper": [2, 515], "tmh_lower": [3, 302], "tmh_upper": [23, 322], "nontmh_lower": [1, 24, 323], "nontmh_upper": [2, 301, 515], "seq": "MGLEALVPLAMIVAIFLLLVDLMHRHQRWAARYPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREAMVTRGEDTADRPPAPIYQVLGFGPRSQGVILSRYGPAWREQRRFSVSTLRNLGLGKKSLEQWVTEEAACLCAAFADQAGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLPHIPALAGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAKKEKAKGSPESSFNDENLRIVVGNLFLAGMVTTSTTLAWGLLLMILHLDVQRGRRVSPGCPIVGTHVCPVRVQQEIDDVIGQVRRPEMGDQAHMPCTTAVIHEVQHFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWKKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVAAGQPRPSHSRVVSFLVTPSPYELCAVPR"}, "PIOS1_HUMAN": {"pac": "A0A0B4J2F0", "gn": "PIGBOS1", "ensembl_id": "ENSG00000225973", "binding_num": 0, "pdb_num": 0, "cyto_lower": [26], "cyto_upper": [54], "extra_lower": [], "extra_upper": [], "tmh_lower": [5], "tmh_upper": [25], "nontmh_lower": [1, 26], "nontmh_upper": [4, 54], "seq": "MFRRLTFAQLLFATVLGIAGGVYIFQPVFEQYAKDQKELKEKMQLVQESEEKKS"},
...
}

Tip

The Json file also returns cytoplasmic and extracellular segments of the extracted transmembrane segments, as indicated by cyto_lower, cyto_upper, extra_lower, and extra_upper. Their combined segments are non-transmembrane segments (nontmh_lower amd nontmh_upper).