The PROSITE database, its status in 1999

doi:10.1093/nar/27.1.215

This Article

	Abstract
	Print PDF (193K)
	Alert me when this article is cited
	Alert me if a correction is posted

Services

	Email this article to a friend
	Similar articles in this journal
	Similar articles in ISI Web of Science
	Similar articles in PubMed
	Alert me to new issues of the journal
	Add to My Personal Archive
	Download to citation manager
	Search for citing articles in: ISI Web of Science (768)
	Request Permissions
	Commercial Re-use Guidelines for Open Access NAR Content

Google Scholar

	Articles by Hofmann, K.
	Articles by Bairoch, A.
	Search for Related Content

PubMed

	PubMed Citation
	Articles by Hofmann, K.
	Articles by Bairoch, A.

Social Bookmarking

	What's this?

Nucleic Acids Research Pages 215-219

The PROSITE database, its status in 1999
Background
Leading Concepts
Format And Document Files
Content Of The Current Release
How To Obtain A Local Copy Of Prosite
   By CD-ROM
   By anonymous FTP
   By Email through the EBI network fileserver
How To Make Use Of Prosite
   Computer programs
   Email servers
   Interactive access to PROSITE using the World Wide Web
References

The PROSITE database, its status in 1999

Kay Hofmann, Philipp Bucher^1,*, Laurent Falquet¹ and Amos Bairoch²

MEMOREC, Stoffel GmbH, Stoeckheimer Weg 1, D-50829 Koeln, Germany, ¹Swiss Institute of Bioinformatics (SIB), Swiss Institute for Experimental Cancer Research (ISREC), CH-1066 Epalinges/Lausanne, Switzerland and ²Swiss Institute of Bioinformatics (SIB), Department of Medical Biochemistry, University of Geneva, 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland

Received October 16, 1998; Accepted October 21, 1998

ABSTRACT

The PROSITE database (http://www.expasy.ch/sprot/prosite.html ) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein (if any) a new sequence belongs, or which known domain(s) it contains.

BACKGROUND

PROSITE (1,2) is a method of identifying what is the function of uncharacterized proteins translated from genomic or cDNA sequences. It consists of a database of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can rapidly and reliably determine to which known family of protein (if any) the new sequence belongs, or which known domain(s) it contains.

In some cases the sequence of an unknown protein is too distantly related to any protein of known structure to detect its resemblance by overall sequence alignment. However, relationships can be revealed by the occurrence in its sequence of a particular cluster of residue types, which is variously known as a pattern, motif, signature or fingerprint. These motifs arise because specific region(s) of a protein which may be important, for example, for their binding properties or for their enzymatic activity are conserved in both structure and sequence. These structural requirements impose very tight constraints on the evolution of this small but important portion(s) of a protein sequence. The use of protein sequence patterns or profiles to determine the function of proteins is becoming very rapidly one of the essential tools of sequence analysis. Many authors (3,4) have recognized this reality. Based on these observations, we decided in 1988, to actively pursue the development of a database of regular expression-like patterns, which would be used to search against sequences of unknown function.

But, while sequence patterns are very useful, there are a number of protein families as well as functional or structural domains that cannot be detected using patterns due to their extreme sequence divergence. Typical examples of important functional domains, which are weakly conserved, are the globins, the immunoglobulin, and the SH2 and SH3 domains. In such domains there are only a few sequence positions which are well conserved. Any attempt to build a consensus pattern for such regions will either fail to pick up a significant proportion of the protein sequences that contain such a region (false negatives) or will pick up too many proteins that do not contain the region (false positives).

The use of techniques based on profiles or weight matrices (the two terms are used synonymously here) allows the detection of such proteins or domains. A profile is a table of position-specific amino acid weights and gap costs. These numbers (also referred to as scores) are used to calculate a similarity score for any alignment between a profile and a sequence, or parts of a profile and a sequence. An alignment with a similarity score higher than or equal to a given cut-off value constitutes a motif occurrence. As with patterns, there may be several matches to a profile in one sequence, but multiple occurrences in the same sequences must be disjoint (non-overlapping) according to a specific definition included in the profile. Another feature that distinguishes patterns from profiles is that the latter are usually not confined to small regions with high sequence similarity. Rather they attempt to characterize a protein family or domain over its entire length.

We therefore started in 1994 to complement the approach based on patterns by gradually adding to PROSITE profile entries. The profile structure (5,6) used in PROSITE is similar to but slightly more general than the one introduced by Gribskov and co-workers (7); additional parameters allow representation of other motif descriptors, including the currently popular hidden Markov models (8). Profiles can be constructed by a large variety of different techniques. The classical method developed by Gribskov and co-workers (9) requires a multiple sequence alignment as input and uses a symbol comparison table to convert residue frequency distributions into weights. Most profiles included in PROSITE are generated by this procedure applying recently described modifications (10,11). In some cases we also applied alternative profile construction methods including structure-based approaches and methods involving hidden Markov modelling.

LEADING CONCEPTS

The design of PROSITE follows five leading concepts.

Completeness. For such a compilation to be helpful in the determination of protein function, it is important that it contains as many biologically meaningful patterns and profiles as possible.

High specificity. In the majority of cases we have chosen patterns or profiles that are specific enough that they do not detect too many unrelated sequences, yet they will detect most, if not all, sequences that clearly belong to the set in consideration.

Documentation. Each of the entries in PROSITE is fully documented; the documentation includes a concise description of the protein family or domain that it is designed to detect as well as a summary of the reasons leading to the development of the pattern or profile.

Periodic reviewing. It is important that each entry be periodically reviewed to ensure that it is still valid.

A very tight relationship with the SWISS-PROT protein sequence data bank (12). Updating of PROSITE and of the annotations of the relevant SWISS-PROT entries are very often done in parallel. Software tools based on PROSITE are used to automatically update the feature table lines of SWISS-PROT entries relevant to the presence and extent of specific domains.

a)

b)

Figure 1. Sample data from PROSITE.

FORMAT AND DOCUMENT FILES

The core of the PROSITE database is composed of two ASCII (text) files. The first file (PROSITE.DAT) is a computer-readable file that contains all the information necessary for programs that make use of PROSITE to scan sequence(s) for the occurrence of the patterns and/or profiles. This file also includes, for each entry described, statistics on the number of hits obtained while scanning for that pattern or profile in SWISS-PROT. Cross-references to the corresponding SWISS-PROT entries are also present in the file. The second file (PROSITE.DOC), which we call the textbook, contains textual information that documents each pattern.

A sample textbook entry is shown (Fig. 1a); this particular entry is linked to two entries in the PROSITE.DAT file: a pattern and a profile (Fig. 1b).

Several document files are also distributed with the database:

PROSUSER.TXT The database user's manual

PROFILE.TXT A detailed description of the syntax for the profiles

PROSITE.LIS A list of PROSITE documentation entries

PROSITE.GET A document on how to obtain a local copy of PROSITE

PROSITE.PRG A description of programs and electronic mail servers that make use of PROSITE

PAUTINDX.TXT An index of authors cited in the PROSITE.DOC file

CONTENT OF THE CURRENT RELEASE

Release 15.0 of PROSITE (July 1998) contains 1014 documentation entries describing 1352 different patterns, rules and profiles/matrices. In addition to these entries, a collection of 241 preliminary profiles is available in the pre-release distribution from the FTP server of the ISREC group (see below). The list of the documentation entries that have been added since the last release of PROSITE (14.0) is provided in Table 1, furthermore, many entries were updated. The database requires ~5 Mb of disk storage space. The present distribution frequency is two releases per year. No restrictions are placed on use or redistribution of the data. Future releases of PROSITE will be copyright (releases up to number 15.0 are not).

HOW TO OBTAIN A LOCAL COPY OF PROSITE

By CD-ROM

PROSITE is distributed on CD-ROM by the EMBL Outstation-the European Bioinformatics Institute (EBI) (13). For all enquiries regarding the subscription and distribution of PROSITE one should contact: The EMBL Outstation-The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Tel: +44 1223 494 444; Fax: +44 1223 494 468; Email: datalib@ebi.ac.uk

Table 1. List of patterns documentation entries that have been added since the last release of PROSITE (14.0)

DNA repair protein radC family signature

recR protein signature

ubiH/COQ6 monooxygenase family signature

ATP phosphoribosyltransferase signature

Prolipoprotein diacylglyceryl transferase signature

Phosphatidate cytidylyltransferase signature

Lipoate-protein ligase B signature

moaA / nifB / pqqE family signature

BCCT family of transporters signature

Flagellar motor protein motA family signature

Protein secA signatures

ATP1G1 / PLM / MAT8 family signature

Protein smpB signature

Uncharacterized protein family UPF0044 signature

Uncharacterized protein family UPF0047 signature

Uncharacterized protein family UPF0054 signature

Uncharacterized protein family UPF0057 signature

By anonymous FTP

If you have access to a computer system linked to the Internet you can obtain PROSITE using FTP (File Transfer Protocol), from the following file servers:

ExPASy (Expert Protein Analysis System) server, Swiss Institute of Bioinformatics (SIB); Internet address: ftp://www.expasy.ch/databases/prosite/

ISREC (Swiss Institute for Experimental Cancer Research) anonymous FTP server, Swiss Institute of Bioinformatics (SIB); Internet address: ftp://ftp.isrec.isb-sib.ch/sib-isrec/profiles/

EBI (European Bioinformatics Institute) anonymous FTP server; Internet address: ftp://ftp.ebi.ac.uk/pub/databases/prosite/

The pre-release collection of profiles is only available from the ISREC FTP server.

By Email through the EBI network fileserver

PROSITE can be obtained from the EBI network fileserver. Detailed instructions on how to make the best use of this service, and in particular on how to obtain PROSITE, can be obtained by sending to the network address netserv{at}ebi.ac.uk the following message:

HELP
HELP PROSITE

HOW TO MAKE USE OF PROSITE

Computer programs

Many academic groups and commercial companies have developed computer programs that make use of the pattern entries in PROSITE. The `PROSITE.PRG' file contains a full list of these programs, their operating system specificity, characteristics as well as information on how to obtain them.

Two software packages are distributed to make use of profile entries:

(i) pftools (version 2.1 in FORTRAN77) written by Philipp Bucher. pfscan loads a sequence from a file and scans it with all (or one) of PROSITE profiles; pfsearch loads a profile from a file and scans for it in a SWISS-PROT database file. These tools are available by anonymous FTP from the server: ftp://ftp.isrec.isb-sib.ch/sib-isrec/pftools . Several versions are available, as well as executables compiled for many unix platforms and for Windows 95/98.

(ii) PrfLib (version 1.0 in ANSI C) written by Nicolas Moeri. scan4prf loads a sequence from a file and scans it with all (or one) of PROSITE profiles; srch4prf loads a profile from a file and scans for it in a SWISS-PROT database file. These tools are available from the server: http://mamac29.epfl.ch/

Email servers

There are many Email servers that are available to molecular biologists (14). This an example of a server taking advantage of the PROSITE database:

Name: MOTIF E-Mail Server on GenomeNet

Organization: Supercomputer Laboratory, Kyoto Institute for Chemical Research, Japan

Description: Allows to rapidly compare a new protein sequence against all patterns stored in PROSITE as well as in the MotifDic library (15).

Server email address: motif{at}genome.ad.jp

Address to report problems: motif-manager{at}genome.ad.jp

Interactive access to PROSITE using the World Wide Web

The most efficient and user-friendly way to browse interactively in PROSITE as well as to analyze a sequence for the occurrence of a pattern or a profile is to use the World-Wide Web (WWW) molecular biology server ExPASy (16). Using a WWW browser, one has access to all the hypertext documents stored on the ExPASy server (as well as many other WWW servers) and also can make use of many sequence analysis software tools.

The ExPASy server may be accessed through its URL which is: http://www.expasy.ch/ . You can directly access to the `top' page of the section of ExPASy that allows you to browse through the PROSITE documentation and data entries by opening the URL: http://www.expasy.ch/sprot/prosite.html

To use the PROSITE patterns and profiles, you can make use of the following software tools.

ScanProsite. Allows the user to either scan a protein sequence-from SWISS-PROT or provided by the user-for the occurrence of patterns stored in PROSITE or to scan the SWISS-PROT and/or TrEMBL database-including weekly releases-for the occurrence of a pattern that can originate from PROSITE or be provided by the user. The URL for ScanProsite is: http://www.expasy.ch/sprot/scnpsite.html

ProfileScan. Allows the user to scan a protein sequence-from SWISS-PROT or provided by the user-for the occurrence of profiles stored in PROSITE. The URL for ProfileScan is: http://www.isrec.isb-sib.ch/software/PFSCAN_form.html

FrameProfileScan. Allows the user to scan a DNA sequence (translated on the fly into protein)-from EMBL or provided by the user-for the occurrence of profiles stored in PROSITE. The URL for FrameProfileScan is: http://www.isrec.isb-sib.ch/software/PFRAMESCAN_form.html

REFERENCES

1. Bairoch,A. and Bucher,P. (1994) Nucleic Acids Res., 22, 3583-3589. MEDLINE Abstract

2. Bairoch,A., Bucher,P. and Hofmann,K. (1997) Nucleic Acids Res., 25, 217-221. MEDLINE Abstract

3. Doolittle,R.F. (1986) Of URFs and ORFs: A Primer On How To Analyze Derived Amino Acid Sequences. University Science Books, Mill Valley, California.

4. Lesk,A.M. (1988) In Lesk,A.M. (ed.), Computational Molecular Biology. Oxford University Press, Oxford, pp. 17-26.

5. Bucher,P. and Bairoch,A. (1994) In Altman,R., Brutlag,D., Karp,P., Lathrop,R. and Searls,D. (eds), ISMB-94; Proceedings Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, pp. 53-61.

6. Bucher,P., Karplus,K., Moeri,N. and Hofmann,K. (1996) Comput. Chem., 20, 3-23. MEDLINE Abstract

7. Gribskov,M., McLachlan,A.D. and Eisenberg,D. (1987) Proc. Natl Acad. Sci. USA, 84, 4355-4358. MEDLINE Abstract

8. Eddy,S.R. (1996) Curr. Opin. Struct. Biol., 6, 361-365. MEDLINE Abstract

9. Gribskov,M., Luethy,R. and Eisenberg,D. (1990) Methods Enzymol., 183, 146-159. MEDLINE Abstract

10. Luethy,R., Xenarios,I. and Bucher,P. (1994) Protein Sci., 3, 139-146.

11. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) Comput. Applic. Biosci., 10, 19-29.

12. Bairoch,A. and Apweiler,R. (1998) Nucleic Acids Res., 26, 38-42. MEDLINE Abstract

13. Stoesser,G., Moseley,M.A., Sleep,J., McGowran,M., Garcia-Pastor,M. and Sterk,P. (1998) Nucleic Acids Res., 26, 8-15. MEDLINE Abstract

14. Henikoff,S. (1993) Trends Biochem. Sci., 18, 267-268. MEDLINE Abstract

15. Ogiwara,A., Uchiyama,I., Seto,Y. and Kanehisa,M. (1992) Protein Engng, 5, 479-488.

16. Appel,R.D., Bairoch,A. and Hochstrasser,D.F. (1994) Trends Biochem. Sci., 19, 258-260. MEDLINE Abstract

*To whom correspondence should be addressed. Tel: +41 21 692 5892; Fax: +41 21 652 6933; Email: philipp.bucher@isrec.unil.ch

This page is run by Oxford University Press, Great Clarendon Street, Oxford OX2 6DP, as part of the OUP Journals
Comments and feedback: www-admin{at}oup.co.uk
Last modification: 9 Dec 1998
Copyright©Oxford University Press, 1998.

CiteULike

Connotea

Del.icio.us What's this?

This article has been cited by other articles:

A. M. M. Abd-Alla, F. Cousserans, A. G. Parker, J. A. Jehle, N. J. Parker, J. M. Vlak, A. S. Robinson, and M. Bergoin
Genome Analysis of a Glossina pallidipes Salivary Gland Hypertrophy Virus Reveals a Novel, Large, Double-Stranded Circular DNA Virus
J. Virol., May 1, 2008; 82(9): 4595 - 4611.
[Abstract] [Full Text] [PDF]

G. Cacciapuoti, M. Porcelli, M. A. Moretti, F. Sorrentino, L. Concilio, V. Zappia, Z.-J. Liu, W. Tempel, F. Schubot, J. P. Rose, et al.
The First Agmatine/Cadaverine Aminopropyl Transferase: Biochemical and Structural Characterization of an Enzyme Involved in Polyamine Biosynthesis in the Hyperthermophilic Archaeon Pyrococcus furiosus
J. Bacteriol., August 15, 2007; 189(16): 6057 - 6067.
[Abstract] [Full Text] [PDF]

S. Chakrabarti and C. J. Lanczycki
Analysis and prediction of functionally important sites in proteins
Protein Sci., January 1, 2007; 16(1): 4 - 13.
[Abstract] [Full Text] [PDF]

D. M. Bulach, R. L. Zuerner, P. Wilson, T. Seemann, A. McGrath, P. A. Cullen, J. Davis, M. Johnson, E. Kuczek, D. P. Alt, et al.
Genome reduction in Leptospira borgpetersenii reflects limited transmission potential
PNAS, September 26, 2006; 103(39): 14560 - 14565.
[Abstract] [Full Text] [PDF]

S. P. Duffy, A. M. Young, B. Morin, C. J. Lucarotti, B. F. Koop, and D. B. Levin
Sequence Analysis and Organization of the Neodiprion abietis Nucleopolyhedrovirus Genome
J. Virol., July 15, 2006; 80(14): 6952 - 6963.
[Abstract] [Full Text] [PDF]

T. Krell, A. J. Molina-Henares, and J. L. Ramos
The IclR family of transcriptional activators and repressors can be defined by a single profile
Protein Sci., May 1, 2006; 15(5): 1207 - 1213.
[Abstract] [Full Text] [PDF]

K. L. Jensen, M. P. Styczynski, I. Rigoutsos, and G. N. Stephanopoulos
A generic motif discovery algorithm for sequential data
Bioinformatics, January 1, 2006; 22(1): 21 - 28.
[Abstract] [Full Text] [PDF]

R. N. Miguel, S. Chen, L. Nikfarjam, S. Kominami, B. Carpenter, C. Dal Pra, C. Betterle, R. Zanchetta, T. Nakamatsu, M. Powell, et al.
Analysis of the interaction between human steroid 21-hydroxylase and various monoclonal antibodies using comparative structural modelling
Eur. J. Endocrinol., December 1, 2005; 153(6): 949 - 961.
[Abstract] [Full Text] [PDF]

J. L. Ramos, M. Martinez-Bueno, A. J. Molina-Henares, W. Teran, K. Watanabe, X. Zhang, M. T. Gallegos, R. Brennan, and R. Tobes
The TetR Family of Transcriptional Repressors
Microbiol. Mol. Biol. Rev., June 1, 2005; 69(2): 326 - 356.
[Abstract] [Full Text] [PDF]

C. Yu, M. Dong, X. Wu, S. Li, S. Huang, J. Su, J. Wei, Y. Shen, C. Mou, X. Xie, et al.
Genes "Waiting" for Recruitment by the Adaptive Immune System: The Insights from Amphioxus
J. Immunol., March 15, 2005; 174(6): 3493 - 3500.
[Abstract] [Full Text] [PDF]

Z. Zhang, S. Kochhar, and M. G. Grigorov
Descriptor-based protein remote homology identification
Protein Sci., February 1, 2005; 14(2): 431 - 444.
[Abstract] [Full Text] [PDF]

S. Guix, S. Caballero, A. Bosch, and R. M. Pinto
C-Terminal nsP1a Protein of Human Astrovirus Colocalizes with the Endoplasmic Reticulum and Viral RNA
J. Virol., December 15, 2004; 78(24): 13627 - 13636.
[Abstract] [Full Text] [PDF]

G. E. Olson, V. P. Winfrey, S. K. NagDas, and M. H. Melner
Region-specific Expression and Secretion of the Fibrinogen-related Protein, fgl2, by Epithelial Cells of the Hamster Epididymis and Its Role in Disposal of Defective Spermatozoa
J. Biol. Chem., December 3, 2004; 279(49): 51266 - 51274.
[Abstract] [Full Text] [PDF]

A. E. Whitfield, D. E. Ullman, and T. L. German
Expression and Characterization of a Soluble Form of Tomato Spotted Wilt Virus Glycoprotein GN
J. Virol., December 1, 2004; 78(23): 13197 - 13206.
[Abstract] [Full Text] [PDF]

A. Kusumoto, S. Seto, J. D. Jaffe, and M. Miyata
Cell surface differentiation of Mycoplasma mobile visualized by surface protein localization
Microbiology, December 1, 2004; 150(12): 4001 - 4008.
[Abstract] [Full Text] [PDF]

J. York, V. Romanowski, M. Lu, and J. H. Nunberg
The Signal Peptide of the Junin Arenavirus Envelope Glycoprotein Is Myristoylated and Forms an Essential Subunit of the Mature G1-G2 Complex
J. Virol., October 1, 2004; 78(19): 10783 - 10792.
[Abstract] [Full Text] [PDF]

Z. Sheng, J. A. Lewis, and W. J. Chirico
Nuclear and Nucleolar Localization of 18-kDa Fibroblast Growth Factor-2 Is Controlled by C-terminal Signals
J. Biol. Chem., September 17, 2004; 279(38): 40153 - 40160.
[Abstract] [Full Text] [PDF]

D. Zhou, J. Xue, O. Gavrialov, and G. G. Haddad
Na+/H+ exchanger 1 deficiency alters gene expression in mouse brain
Physiol Genomics, August 11, 2004; 18(3): 331 - 339.
[Abstract] [Full Text] [PDF]

A. Hidalgo, L. Betancor, R. Moreno, O. Zafra, F. Cava, R. Fernandez-Lafuente, J. M. Guisan, and J. Berenguer
Thermus thermophilus as a Cell Factory for the Production of a Thermophilic Mn-Dependent Catalase Which Fails To Be Synthesized in an Active Form in Escherichia coli
Appl. Envir. Microbiol., July 1, 2004; 70(7): 3839 - 3844.
[Abstract] [Full Text] [PDF]

B. Rost, G. Yachdav, and J. Liu
The PredictProtein server
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W321 - W326.
[Abstract] [Full Text] [PDF]

S. E. Bondos, D. J. Catanese Jr., X.-X. Tan, A. Bicknell, L. Li, and K. S. Matthews
Hox Transcription Factor Ultrabithorax Ib Physically and Genetically Interacts with Disconnected Interacting Protein 1, a Double-stranded RNA-binding Protein
J. Biol. Chem., June 18, 2004; 279(25): 26433 - 26444.
[Abstract] [Full Text] [PDF]

M. Sunde, K. C. Y. McGrath, L. Young, J. M. Matthews, E. L. Chua, J. P. Mackay, and A. K. Death
TC-1 Is a Novel Tumorigenic and Natively Disordered Protein Associated with Thyroid Cancer
Cancer Res., April 15, 2004; 64(8): 2766 - 2773.
[Abstract] [Full Text] [PDF]

E. J. Burge, D. T. Gauthier, C. A. Ottinger, and P. A. Van Veld
Mycobacterium-Inducible Nramp in Striped Bass (Morone saxatilis)
Infect. Immun., March 1, 2004; 72(3): 1626 - 1636.
[Abstract] [Full Text] [PDF]

I. Remy and S. W. Michnick
Regulation of Apoptosis by the Ft1 Protein, a New Modulator of Protein Kinase B/Akt
Mol. Cell. Biol., February 15, 2004; 24(4): 1493 - 1504.
[Abstract] [Full Text] [PDF]

K. Grunberg, E.-C. Muller, A. Otto, R. Reszka, D. Linder, M. Kube, R. Reinhardt, and D. Schuler
Biochemical and Proteomic Analysis of the Magnetosome Membrane in Magnetospirillum gryphiswaldense
Appl. Envir. Microbiol., February 1, 2004; 70(2): 1040 - 1050.
[Abstract] [Full Text] [PDF]

G. Cecchetto, S. Amillis, G. Diallinas, C. Scazzocchio, and C. Drevet
The AzgA Purine Transporter of Aspergillus nidulans: CHARACTERIZATION OF A PROTEIN BELONGING TO A NEW PHYLOGENETIC CLUSTER
J. Biol. Chem., January 30, 2004; 279(5): 3132 - 3141.
[Abstract] [Full Text] [PDF]

S. Lievens, S. Goormachtig, and M. Holsters
Nodule-enhanced protease inhibitor gene: emerging patterns of gene expression in nodule development on Sesbania rostrata
J. Exp. Bot., January 1, 2004; 55(394): 89 - 97.
[Abstract] [Full Text] [PDF]

M. Wandrey, B. Trevaskis, N. Brewin, and M. K. Udvardi
Molecular and Cell Biology of a Family of Voltage-Dependent Anion Channel Porins in Lotus japonicus
Plant Physiology, January 1, 2004; 134(1): 182 - 193.
[Abstract] [Full Text] [PDF]

L. A. Salem, C. L. Boucher, and T. M. Menees
Relationship between RNA Lariat Debranching and Ty1 Element Retrotransposition
J. Virol., December 1, 2003; 77(23): 12795 - 12806.
[Abstract] [Full Text] [PDF]

K. A. Kaczorowski and P. H. Quail
Arabidopsis PSEUDO-RESPONSE REGULATOR7 Is a Signaling Intermediate in Phytochrome-Regulated Seedling Deetiolation and Phasing of the Circadian Clock
PLANT CELL, November 1, 2003; 15(11): 2654 - 2665.
[Abstract] [Full Text] [PDF]

K. E. Nolan, R. R. Irwanto, and R. J. Rose
Auxin Up-Regulates MtSERK1 Expression in Both Medicago truncatula Root-Forming and Embryogenic Cultures
Plant Physiology, September 1, 2003; 133(1): 218 - 230.
[Abstract] [Full Text] [PDF]

K. M. Fenster, K. L. Parkin, and J. L. Steele
Nucleotide Sequencing, Purification, and Biochemical Properties of an Arylesterase from Lactobacillus casei LILA
J Dairy Sci, August 1, 2003; 86(8): 2547 - 2557.
[Abstract] [Full Text] [PDF]

E. F. Hendriks, A. Abdul-Razak, and K. R. Matthews
tbCPSF30 Depletion by RNA Interference Disrupts Polycistronic RNA Processing in Trypanosoma brucei
J. Biol. Chem., July 11, 2003; 278(29): 26870 - 26878.
[Abstract] [Full Text] [PDF]

U. Johnsen, T. Hansen, and P. Schonheit
Comparative Analysis of Pyruvate Kinases from the Hyperthermophilic Archaea Archaeoglobus fulgidus, Aeropyrum pernix, and Pyrobaculum aerophilum and the Hyperthermophilic Bacterium Thermotoga maritima: UNUSUAL REGULATORY PROPERTIES IN HYPERTHERMOPHILIC ARCHAEA
J. Biol. Chem., July 3, 2003; 278(28): 25417 - 25427.
[Abstract] [Full Text] [PDF]

B. Rost and J. Liu
The PredictProtein server
Nucleic Acids Res., July 1, 2003; 31(13): 3300 - 3304.
[Abstract] [Full Text] [PDF]

R. Nair and B. Rost
LOC3D: annotate sub-cellular localization for protein structures
Nucleic Acids Res., July 1, 2003; 31(13): 3337 - 3340.
[Abstract] [Full Text] [PDF]

J. L. Gardy, C. Spencer, K. Wang, M. Ester, G. E. Tusnady, I. Simon, S. Hua, K. deFays, C. Lambert, K. Nakai, et al.
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria
Nucleic Acids Res., July 1, 2003; 31(13): 3613 - 3617.
[Abstract] [Full Text] [PDF]

J. McDermott and R. Samudrala
Bioverse: functional, structural and contextual annotation of proteins and proteomes
Nucleic Acids Res., July 1, 2003; 31(13): 3736 - 3737.
[Abstract] [Full Text] [PDF]

N. Delgado, J. Xue, J.-J. Yu, C.-Y. Hung, and G. T. Cole
A Recombinant {beta}-1,3-Glucanosyltransferase Homolog of Coccidioides posadasii Protects Mice against Coccidioidomycosis
Infect. Immun., June 1, 2003; 71(6): 3010 - 3019.
[Abstract] [Full Text] [PDF]

E. M. Hrabak, C. W.M. Chan, M. Gribskov, J. F. Harper, J. H. Choi, N. Halford, J. Kudla, S. Luan, H. G. Nimmo, M. R. Sussman, et al.
The Arabidopsis CDPK-SnRK Superfamily of Protein Kinases
Plant Physiology, June 1, 2003; 132(2): 666 - 680.
[Abstract] [Full Text] [PDF]

O. Nufer, S. Mitrovic, and H.-P. Hauri
Profile-based Data Base Scanning for Animal L-type Lectins and Characterization of VIPL, a Novel VIP36-like Endoplasmic Reticulum Protein
J. Biol. Chem., April 25, 2003; 278(18): 15886 - 15896.
[Abstract] [Full Text] [PDF]

E. Schondorf, U. Bahr, M. Handermann, and G. Darai
Characterization of the Complete Genome of the Tupaia (Tree Shrew) Adenovirus
J. Virol., April 1, 2003; 77(7): 4345 - 4356.
[Abstract] [Full Text] [PDF]

K. M. Fenster, K. L. Parkin, and J. L. Steele
Intracellular Esterase from Lactobacillus casei LILA: Nucleotide Sequencing, Purification, and Characterization
J Dairy Sci, April 1, 2003; 86(4): 1118 - 1129.
[Abstract] [Full Text] [PDF]

M. Okamoto, J. J. Vidmar, and A. D. M. Glass
Regulation of NRT1 and NRT2 Gene Families of Arabidopsis thaliana: Responses to Nitrate Provision
Plant Cell Physiol., March 15, 2003; 44(3): 304 - 317.
[Abstract] [Full Text] [PDF]

PROSUSER.TXT		The database user's manual
PROFILE.TXT		A detailed description of the syntax for the profiles
PROSITE.LIS		A list of PROSITE documentation entries
PROSITE.GET		A document on how to obtain a local copy of PROSITE
PROSITE.PRG		A description of programs and electronic mail servers that make use of PROSITE
PAUTINDX.TXT		An index of authors cited in the PROSITE.DOC file

Name:		MOTIF E-Mail Server on GenomeNet
Organization:		Supercomputer Laboratory, Kyoto Institute for Chemical Research, Japan
Description:		Allows to rapidly compare a new protein sequence against all patterns stored in PROSITE as well as in the MotifDic library (15).
Server email address:		motif{at}genome.ad.jp
Address to report problems:		motif-manager{at}genome.ad.jp

				G. Cacciapuoti, M. Porcelli, M. A. Moretti, F. Sorrentino, L. Concilio, V. Zappia, Z.-J. Liu, W. Tempel, F. Schubot, J. P. Rose, et al. The First Agmatine/Cadaverine Aminopropyl Transferase: Biochemical and Structural Characterization of an Enzyme Involved in Polyamine Biosynthesis in the Hyperthermophilic Archaeon Pyrococcus furiosus J. Bacteriol., August 15, 2007; 189(16): 6057 - 6067. [Abstract] [Full Text] [PDF]

				S. Chakrabarti and C. J. Lanczycki Analysis and prediction of functionally important sites in proteins Protein Sci., January 1, 2007; 16(1): 4 - 13. [Abstract] [Full Text] [PDF]

				D. M. Bulach, R. L. Zuerner, P. Wilson, T. Seemann, A. McGrath, P. A. Cullen, J. Davis, M. Johnson, E. Kuczek, D. P. Alt, et al. Genome reduction in Leptospira borgpetersenii reflects limited transmission potential PNAS, September 26, 2006; 103(39): 14560 - 14565. [Abstract] [Full Text] [PDF]

				S. P. Duffy, A. M. Young, B. Morin, C. J. Lucarotti, B. F. Koop, and D. B. Levin Sequence Analysis and Organization of the Neodiprion abietis Nucleopolyhedrovirus Genome J. Virol., July 15, 2006; 80(14): 6952 - 6963. [Abstract] [Full Text] [PDF]

				T. Krell, A. J. Molina-Henares, and J. L. Ramos The IclR family of transcriptional activators and repressors can be defined by a single profile Protein Sci., May 1, 2006; 15(5): 1207 - 1213. [Abstract] [Full Text] [PDF]

				K. L. Jensen, M. P. Styczynski, I. Rigoutsos, and G. N. Stephanopoulos A generic motif discovery algorithm for sequential data Bioinformatics, January 1, 2006; 22(1): 21 - 28. [Abstract] [Full Text] [PDF]

				R. N. Miguel, S. Chen, L. Nikfarjam, S. Kominami, B. Carpenter, C. Dal Pra, C. Betterle, R. Zanchetta, T. Nakamatsu, M. Powell, et al. Analysis of the interaction between human steroid 21-hydroxylase and various monoclonal antibodies using comparative structural modelling Eur. J. Endocrinol., December 1, 2005; 153(6): 949 - 961. [Abstract] [Full Text] [PDF]

				J. L. Ramos, M. Martinez-Bueno, A. J. Molina-Henares, W. Teran, K. Watanabe, X. Zhang, M. T. Gallegos, R. Brennan, and R. Tobes The TetR Family of Transcriptional Repressors Microbiol. Mol. Biol. Rev., June 1, 2005; 69(2): 326 - 356. [Abstract] [Full Text] [PDF]

				C. Yu, M. Dong, X. Wu, S. Li, S. Huang, J. Su, J. Wei, Y. Shen, C. Mou, X. Xie, et al. Genes "Waiting" for Recruitment by the Adaptive Immune System: The Insights from Amphioxus J. Immunol., March 15, 2005; 174(6): 3493 - 3500. [Abstract] [Full Text] [PDF]

				Z. Zhang, S. Kochhar, and M. G. Grigorov Descriptor-based protein remote homology identification Protein Sci., February 1, 2005; 14(2): 431 - 444. [Abstract] [Full Text] [PDF]

				S. Guix, S. Caballero, A. Bosch, and R. M. Pinto C-Terminal nsP1a Protein of Human Astrovirus Colocalizes with the Endoplasmic Reticulum and Viral RNA J. Virol., December 15, 2004; 78(24): 13627 - 13636. [Abstract] [Full Text] [PDF]

				G. E. Olson, V. P. Winfrey, S. K. NagDas, and M. H. Melner Region-specific Expression and Secretion of the Fibrinogen-related Protein, fgl2, by Epithelial Cells of the Hamster Epididymis and Its Role in Disposal of Defective Spermatozoa J. Biol. Chem., December 3, 2004; 279(49): 51266 - 51274. [Abstract] [Full Text] [PDF]

				A. E. Whitfield, D. E. Ullman, and T. L. German Expression and Characterization of a Soluble Form of Tomato Spotted Wilt Virus Glycoprotein GN J. Virol., December 1, 2004; 78(23): 13197 - 13206. [Abstract] [Full Text] [PDF]

				A. Kusumoto, S. Seto, J. D. Jaffe, and M. Miyata Cell surface differentiation of Mycoplasma mobile visualized by surface protein localization Microbiology, December 1, 2004; 150(12): 4001 - 4008. [Abstract] [Full Text] [PDF]

				J. York, V. Romanowski, M. Lu, and J. H. Nunberg The Signal Peptide of the Junin Arenavirus Envelope Glycoprotein Is Myristoylated and Forms an Essential Subunit of the Mature G1-G2 Complex J. Virol., October 1, 2004; 78(19): 10783 - 10792. [Abstract] [Full Text] [PDF]

				Z. Sheng, J. A. Lewis, and W. J. Chirico Nuclear and Nucleolar Localization of 18-kDa Fibroblast Growth Factor-2 Is Controlled by C-terminal Signals J. Biol. Chem., September 17, 2004; 279(38): 40153 - 40160. [Abstract] [Full Text] [PDF]

				D. Zhou, J. Xue, O. Gavrialov, and G. G. Haddad Na+/H+ exchanger 1 deficiency alters gene expression in mouse brain Physiol Genomics, August 11, 2004; 18(3): 331 - 339. [Abstract] [Full Text] [PDF]

				A. Hidalgo, L. Betancor, R. Moreno, O. Zafra, F. Cava, R. Fernandez-Lafuente, J. M. Guisan, and J. Berenguer Thermus thermophilus as a Cell Factory for the Production of a Thermophilic Mn-Dependent Catalase Which Fails To Be Synthesized in an Active Form in Escherichia coli Appl. Envir. Microbiol., July 1, 2004; 70(7): 3839 - 3844. [Abstract] [Full Text] [PDF]

				B. Rost, G. Yachdav, and J. Liu The PredictProtein server Nucleic Acids Res., July 1, 2004; 32(suppl_2): W321 - W326. [Abstract] [Full Text] [PDF]

				S. E. Bondos, D. J. Catanese Jr., X.-X. Tan, A. Bicknell, L. Li, and K. S. Matthews Hox Transcription Factor Ultrabithorax Ib Physically and Genetically Interacts with Disconnected Interacting Protein 1, a Double-stranded RNA-binding Protein J. Biol. Chem., June 18, 2004; 279(25): 26433 - 26444. [Abstract] [Full Text] [PDF]

				M. Sunde, K. C. Y. McGrath, L. Young, J. M. Matthews, E. L. Chua, J. P. Mackay, and A. K. Death TC-1 Is a Novel Tumorigenic and Natively Disordered Protein Associated with Thyroid Cancer Cancer Res., April 15, 2004; 64(8): 2766 - 2773. [Abstract] [Full Text] [PDF]

				E. J. Burge, D. T. Gauthier, C. A. Ottinger, and P. A. Van Veld Mycobacterium-Inducible Nramp in Striped Bass (Morone saxatilis) Infect. Immun., March 1, 2004; 72(3): 1626 - 1636. [Abstract] [Full Text] [PDF]

				I. Remy and S. W. Michnick Regulation of Apoptosis by the Ft1 Protein, a New Modulator of Protein Kinase B/Akt Mol. Cell. Biol., February 15, 2004; 24(4): 1493 - 1504. [Abstract] [Full Text] [PDF]

				K. Grunberg, E.-C. Muller, A. Otto, R. Reszka, D. Linder, M. Kube, R. Reinhardt, and D. Schuler Biochemical and Proteomic Analysis of the Magnetosome Membrane in Magnetospirillum gryphiswaldense Appl. Envir. Microbiol., February 1, 2004; 70(2): 1040 - 1050. [Abstract] [Full Text] [PDF]

				G. Cecchetto, S. Amillis, G. Diallinas, C. Scazzocchio, and C. Drevet The AzgA Purine Transporter of Aspergillus nidulans: CHARACTERIZATION OF A PROTEIN BELONGING TO A NEW PHYLOGENETIC CLUSTER J. Biol. Chem., January 30, 2004; 279(5): 3132 - 3141. [Abstract] [Full Text] [PDF]

				S. Lievens, S. Goormachtig, and M. Holsters Nodule-enhanced protease inhibitor gene: emerging patterns of gene expression in nodule development on Sesbania rostrata J. Exp. Bot., January 1, 2004; 55(394): 89 - 97. [Abstract] [Full Text] [PDF]

				M. Wandrey, B. Trevaskis, N. Brewin, and M. K. Udvardi Molecular and Cell Biology of a Family of Voltage-Dependent Anion Channel Porins in Lotus japonicus Plant Physiology, January 1, 2004; 134(1): 182 - 193. [Abstract] [Full Text] [PDF]

				L. A. Salem, C. L. Boucher, and T. M. Menees Relationship between RNA Lariat Debranching and Ty1 Element Retrotransposition J. Virol., December 1, 2003; 77(23): 12795 - 12806. [Abstract] [Full Text] [PDF]