Fetch data

Cath[1] is a protein structural classification database that currently has more than 100 million protein domains that are classified into thousands of superfamilies.

TMKit provides a module, tmkit.cath, to access the Cath database.

Links to domain and family

TMKit accesses the information about the domains and families of a protein by using parameter id. For example, if you are interested in protein 1cuk chain A, we can generate the links to its domain 01. Thus, we can do it this way.

import tmkit as tmk

res = tmk.cath.summary_by_id(
    id='1cukA01'
)
print(res)

Attributes

id represents protein name + chain + domain, e.g., 1cukA01 (1cuk+A+01)

Output

The result is made in JSON format as shown below. The detailed information about its domain can be seen by opening the link that follows it.

{'domain': 'http://www.cathdb.info/version/v4_2_0/api/rest/domain_summary/1cukA01', 'funfam': 'http://www.cathdb.info/version/v4_2_0/api/rest/superfamily/1.10.8.10/funfam/1cukA01', 'superfamily': 'http://www.cathdb.info/version/v4_2_0/api/rest/superfamily/1cukA01'}

Details about domain and family

Similarly, we run the following code.

import tmkit as tmk

res = tmk.cath.fetch_by_id(
    id='1cukA01'
)
print(res)

Output

The detailed information about its domain is made in JSON format as shown below.

{'atom_length': 66, 's35_id': '2.40.50.140.109', 'combs_segments': [{'pdb_code': '1cuk', 'stop': '66', 'chain_code': 'A', 'start': '1'}], 'residues': [{'pdbres': '1', 'seqres': 1, 'aa': 'M'}, {'pdbres': '2', 'seqres': 2, 'aa': 'I'}, {'pdbres': '3', 'seqres': 3, 'aa': 'G'}, {'pdbres': '4', 'seqres': 4, 'aa': 'R'}, {'pdbres': '5', 'seqres': 5, 'aa': 'L'}, {'pdbres': '6', 'seqres': 6, 'aa': 'R'}, {'pdbres': '7', 'seqres': 7, 'aa': 'G'}, {'pdbres': '8', 'seqres': 8, 'aa': 'I'}, {'pdbres': '9', 'seqres': 9, 'aa': 'I'}, {'pdbres': '10', 'seqres': 10, 'aa': 'I'}, {'pdbres': '11', 'seqres': 11, 'aa': 'E'}, {'pdbres': '12', 'seqres': 12, 'aa': 'K'}, {'pdbres': '13', 'seqres': 13, 'aa': 'Q'}, {'pdbres': '14', 'seqres': 14, 'aa': 'P'}, {'pdbres': '15', 'seqres': 15, 'aa': 'P'}, {'pdbres': '16', 'seqres': 16, 'aa': 'L'}, {'pdbres': '17', 'seqres': 17, 'aa': 'V'}, {'pdbres': '18', 'seqres': 18, 'aa': 'L'}, {'pdbres': '19', 'seqres': 19, 'aa': 'I'}, {'pdbres': '20', 'seqres': 20, 'aa': 'E'}, {'pdbres': '21', 'seqres': 21, 'aa': 'V'}, {'pdbres': '22', 'seqres': 22, 'aa': 'G'}, {'pdbres': '23', 'seqres': 23, 'aa': 'G'}, {'pdbres': '24', 'seqres': 24, 'aa': 'V'}, {'pdbres': '25', 'seqres': 25, 'aa': 'G'}, {'pdbres': '26', 'seqres': 26, 'aa': 'Y'}, {'pdbres': '27', 'seqres': 27, 'aa': 'E'}, {'pdbres': '28', 'seqres': 28, 'aa': 'V'}, {'pdbres': '29', 'seqres': 29, 'aa': 'H'}, {'pdbres': '30', 'seqres': 30, 'aa': 'M'}, {'pdbres': '31', 'seqres': 31, 'aa': 'P'}, {'pdbres': '32', 'seqres': 32, 'aa': 'M'}, {'pdbres': '33', 'seqres': 33, 'aa': 'T'}, {'pdbres': '34', 'seqres': 34, 'aa': 'C'}, {'pdbres': '35', 'seqres': 35, 'aa': 'F'}, {'pdbres': '36', 'seqres': 36, 'aa': 'Y'}, {'pdbres': '37', 'seqres': 37, 'aa': 'E'}, {'pdbres': '38', 'seqres': 38, 'aa': 'L'}, {'pdbres': '39', 'seqres': 39, 'aa': 'P'}, {'pdbres': '40', 'seqres': 40, 'aa': 'E'}, {'pdbres': '41', 'seqres': 41, 'aa': 'A'}, {'pdbres': '42', 'seqres': 42, 'aa': 'G'}, {'pdbres': '43', 'seqres': 43, 'aa': 'Q'}, {'pdbres': '44', 'seqres': 44, 'aa': 'E'}, {'pdbres': '45', 'seqres': 45, 'aa': 'A'}, {'pdbres': '46', 'seqres': 46, 'aa': 'I'}, {'pdbres': '47', 'seqres': 47, 'aa': 'V'}, {'pdbres': '48', 'seqres': 48, 'aa': 'F'}, {'pdbres': '49', 'seqres': 49, 'aa': 'T'}, {'pdbres': '50', 'seqres': 50, 'aa': 'H'}, {'pdbres': '51', 'seqres': 51, 'aa': 'F'}, {'pdbres': '52', 'seqres': 52, 'aa': 'V'}, {'pdbres': '53', 'seqres': 53, 'aa': 'V'}, {'pdbres': '54', 'seqres': 54, 'aa': 'R'}, {'pdbres': '55', 'seqres': 55, 'aa': 'E'}, {'pdbres': '56', 'seqres': 56, 'aa': 'D'}, {'pdbres': '57', 'seqres': 57, 'aa': 'A'}, {'pdbres': '58', 'seqres': 58, 'aa': 'Q'}, {'pdbres': '59', 'seqres': 59, 'aa': 'L'}, {'pdbres': '60', 'seqres': 60, 'aa': 'L'}, {'pdbres': '61', 'seqres': 61, 'aa': 'Y'}, {'pdbres': '62', 'seqres': 62, 'aa': 'G'}, {'pdbres': '63', 'seqres': 63, 'aa': 'F'}, {'pdbres': '64', 'seqres': 64, 'aa': 'N'}, {'pdbres': '65', 'seqres': 65, 'aa': 'N'}, {'pdbres': '66', 'seqres': 66, 'aa': 'K'}], 'funfam_number': 58874, 'cath_id': '2.40.50.140.109.1.1.1.1', 'superfamily_id': '2.40.50.140', 'domain_id': '1cukA01', 'pdb_segments': [{'pdb_code': '1cuk', 'stop': '66', 'chain_code': 'A', 'start': '1'}], 'ssg5_number': 12, 'ec_terms': [{'alternative_names': None, 'cofactors': None, 'reaction': 'ATP + H(2)O = ADP + phosphate.', 'comments': "-!- DNA helicases utilize the energy from ATP hydrolysis to unwind double-stranded DNA. -!- Some of them unwind duplex DNA with a 3' to 5' polarity (1,3,5,8), other show 5' to 3' polarity (10,11,12,13) or unwind DNA in both directions (14,15). -!- Some helicases unwind DNA as well as RNA (4,9). -!- May be identical with EC 3.6.4.13 (RNA helicase).", 'description': 'DNA helicase.', 'ec_code': '3.6.4.12', 'uniprot_acc': 'P0A809'}], 'go_terms': [{'term_type': 'biological_process', 'go_acc': 'GO:0000725', 'name': 'recombinational repair', 'evidence': 'IMP', 'definition': 'A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.'}, {'term_type': 'molecular_function', 'go_acc': 'GO:0009378', 'name': 'four-way junction helicase activity', 'evidence': 'IDA', 'definition': 'Catalysis of the unwinding of the DNA helix of DNA containing four-way junctions, including Holliday junctions.'}, {'term_type': 'cellular_component', 'go_acc': 'GO:0009379', 'name': 'Holliday junction helicase complex', 'evidence': 'IDA', 'definition': 'A DNA helicase complex that forms part of a Holliday junction resolvase complex, where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA.'}, {'term_type': 'biological_process', 'go_acc': 'GO:0009432', 'name': 'SOS response', 'evidence': 'IEP', 'definition': 'An error-prone process for repairing damaged microbial DNA.'}, {'term_type': 'biological_process', 'go_acc': 'GO:0009432', 'name': 'SOS response', 'evidence': 'RCA', 'definition': 'An error-prone process for repairing damaged microbial DNA.'}, {'term_type': 'cellular_component', 'go_acc': 'GO:0048476', 'name': 'Holliday junction resolvase complex', 'evidence': 'IDA', 'definition': 'A protein complex that mediates the conversion of a Holliday junction into two separate duplex DNA molecules; the complex includes a single- or multisubunit helicase that catalyzes the extension of heteroduplex DNA by branch migration and a nuclease that resolves the junction by nucleolytic cleavage.'}], 'pdb_code': '1cuk', 'ssg9_number': 12, 'atom_sequence': 'MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNK', 'combs_sequence': 'MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNK'}

The entire Cath database

If you would like to access the domain information for all available proteins, we can use the tmk.cath.read function. Before that, we need to retrieve a Cath database. By default, we get the newest version and save it in ./data/cath/ as shown below.

import tmkit as tmk

tmk.cath.download(
    version='newest',
    sv_fp='./data/cath/'
)

The file will be automatically decompressed into ./data/cath/cath-b-newest-all.txt.

import tmkit as tmk

df = tmk.cath.read(
    cath_fpn='./data/cath/cath-b-newest-all.txt',
    groupby='version',
    group='v4_2_0',
)
print(df)

Attributes

Attribute	Description
version	version of the Cath database
sv_fpn	path to save the Cath database
cath_fpn	path to the downloaded Cath database
groupby	metric used to group data, e.g., version. There are 4 metrics in total, i.e., domain, version, superfamily, and bound
group	value of a metric. For example, if version is chosen, there are two, namely, v4_2_0 and putative

Output

The result is made as a Pandas dataframe.

======>reading CATH...
======>CATH features are:
=========>No.1: domain
=========>No.2: version
=========>No.3: superfamily
=========>No.4: bound
         domain version  superfamily    bound
0       101mA00  v4_2_0  1.10.490.10  0-153:A
1       102lA00  v4_2_0  1.10.530.40  1-162:A
2       102mA00  v4_2_0  1.10.490.10  0-153:A
3       103lA00  v4_2_0  1.10.530.40  1-162:A
4       103mA00  v4_2_0  1.10.490.10  0-153:A
...         ...     ...          ...      ...
439144  9xiaA00  v4_2_0  3.20.20.150  1-387:A
439145  9ximA00  v4_2_0  3.20.20.150  3-394:A
439146  9ximB00  v4_2_0  3.20.20.150  3-394:B
439147  9ximC00  v4_2_0  3.20.20.150  4-394:C
439148  9ximD00  v4_2_0  3.20.20.150  3-394:D

[439149 rows x 4 columns]

---

[1]

Sillitoe I, Bordin N, Dawson N, Waman VP, Ashford P, Scholes HM, Pang CSM, Woodridge L, Rauer C, Sen N, Abbasian M, Le Cornu S, Lam SD, Berka K, Varekova IH, Svobodova R, Lees J, Orengo CA. CATH: increased structural coverage of functional space. Nucleic Acids Res. 2021 Jan 8;49(D1):D266-D273. doi: 10.1093/nar/gkaa1079. PMID: 33237325; PMCID: PMC7778904.