footprintDB is a database of curated regulatory sequences and their associated transcription factors (TFs). It systematically annotates the binding interfaces of the TFs, the key residues responsible for specific binding, by exploiting protein-DNA complexes at the Protein Data Bank.
Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues. It has been described at:
- [1] https://doi.org/10.1093/bioinformatics/btt663
- [2] https://doi.org/10.1186/1471-2164-15-317
- [3] https://link.springer.com/protocol/10.1007%2F978-1-4939-6396-6_17
- [4] https://link.springer.com/chapter/10.1007/978-3-642-28062-7_8
The footprintDB database is also intergrated with RSAT, please see https://github.com/rsa-tools/motif_databases
This repo documents a REST interface for users wanting to programatically match their own protein sequence against footprintDB.
The actual server code is in file rest_server.pl and requires Perl module Mojolicious::Lite.
The URL of the production server is http://footprintdb.eead.csic.es:8080/protein
To query the API you need curl and one or more protein sequences (queries) in JSON format:
curl -X POST -H "Content-Type: application/json" -d '{"q1":"MVAKVKRDGEVLVAAATGDSEEQDDLVLPGFRFHPTDEELVTFYLRRKVARKPLSMEIIKEMDIYKHDPWDLPKASTVGGEKEWYFFCLRGRKYRNSIRPNRVTGSGFWKATGIDRPIYPAAAGESVGLKKSLVYYRGSAGKGAKTDWMMHEFRLPPAASSPSTQEAVEVWTICRIFKRNIAYKKRQPAGSNAPPPPLAESSSNTGSFESGGGGDDGEYMNCLPVPVPATAAVVPRQQHRIGSMLNGGGVTASGSSFFREVGVHGQQFQGHWLNRFAAPEIERKPQLLGSSAMTIAFHQNDQTAATNECYKDGHWDEIARFMEVNDPTVLYDCRYA","q2":"IYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIEN"}' http://footprintdb.eead.csic.es:8080/protein
This will produce text output in TRANSFAC format with predicted DNA motifs for each input sequence, with links to the actual entries in the database. The key quality indicators are BLASTP e-value and interface identity and similarity, read more at [1-2]:
AC protein_query:q1 match:1
XX
ID q1|NAC74|EEADannot 2025-07-22
XX
DT 29.07.2025 (predicted)
XX
NA EEAD0487
XX
DE EEAD0487
XX
OS Zea mays
XX
BF ZmNAC74;NACTF74;GRMZM2G112548_T01; Species: Zea mays
XX
PO A C G T
01 0.242 0.482 0.139 0.137 c
02 0.335 0.039 0.593 0.033 r
03 0.447 0.045 0.430 0.078 r
04 0.000 0.472 0.000 0.528 y
05 0.112 0.000 0.831 0.057 G
06 0.122 0.513 0.342 0.023 s
07 0.018 0.982 0.000 0.000 C
08 0.001 0.000 0.999 0.000 G
09 0.002 0.000 0.186 0.812 T
10 0.228 0.218 0.428 0.126 g
11 0.186 0.374 0.280 0.160 s
XX
CC footprintDB match: BLASTP e-value=0.0 interface identity=8/8 similarity=8/8
CC footprintDB Pfam domains: PF02365 (No apical meristem (NAM) protein)
CC footprintDB library: EEADannot 2025-07-22
XX
LN https://footprintdb.eead.csic.es/index.php?tf=21873
XX
//
...
AC protein_query:q2 match:1
XX
ID q2|ECK120004795|RegulonDB 7.5
XX
DT 29.07.2025 (predicted)
XX
NA FNR
XX
DE FNR
XX
OS ECK12
XX
BF FNR; Species: ECK12
XX
PO A C G T
01 17 8 10 48 t
02 5 8 6 64 T
03 13 10 58 2 G
04 47 14 8 14 a
05 10 3 13 57 T
06 17 28 3 35 y
07 28 10 16 29 w
08 48 12 11 12 a
09 20 23 11 29 y
10 66 0 11 6 A
11 4 0 0 79 T
12 0 72 5 6 C
13 80 1 0 2 A
14 73 8 0 2 A
XX
CC footprintDB match: BLASTP e-value=2e-38 interface identity=8/8 similarity=8/8
CC footprintDB Pfam domains: PF13545 (Crp-like helix-turn-helix domain) / PF00325 (Bacterial regulatory proteins, crp family)
CC footprintDB library: RegulonDB 7.5
XX
LN https://footprintdb.eead.csic.es/index.php?tf=5989
XX
//
On March 2023 the original SOAP Web Services interface was deprecated, you can still check the relevant files at old.SOAP.
Citation: Sebastian A, Contreras-Moreira B (2014) footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics 30, 258-65. https://doi.org/10.1093/bioinformatics/btt663
Funding: ARAID, CSIC [2020AEP119, FAS2022_052, INFRA24018] and the 2008 Euro Research Program [EUI2008-03612].