1. Database 5: protein domain/family

2. Protein domain/family: some definitions Most proteins have « modular » structures Estimation: ~ 3 domains / protein Domains (conserved sequences or structures) are identified by multiple sequence alignments Domains can be defined by different methods: Pattern (regular expression); used for very conserved domains Profiles (weighted matrices): two-dimensional tables of position specific match-, gap-, and insertion-scores, derived from aligned sequence families; used for less conserved domains Hidden Markov Model (HMM); probabilistic models; an other method to generate profiles.

3. [LIVM]-[ST]-A-[STAG]-H-C Pattern-Profile Profile: Pattern: Yes or no ID TRYPSIN_DOM; MATRIX. AC PS50240; DT DEC-2001 (CREATED); DEC-2001 (DATA UPDATE); DEC-2001 (INFO UPDATE). DE Serine proteases, trypsin domain profile. MA /GENERAL_SPEC: ALPHABET='ABCDEFGHIKLMNPQRSTVWYZ'; LENGTH=234; MA /DISJOINT: DEFINITION=PROTECT; N1=6; N2=229; MA /NORMALIZATION: MODE=1; FUNCTION=LINEAR; R1=0.0169; R2=0.00836256; TEXT='-LogE'; MA /CUT_OFF: LEVEL=0; SCORE=1134; N_SCORE=9.5; MODE=1; TEXT='!'; MA /CUT_OFF: LEVEL=-1; SCORE=775; N_SCORE=6.5; MODE=1; TEXT='?'; MA /DEFAULT: M0=-9; D=-20; I=-20; B1=-60; E1=-60; MI=-105; MD=-105; IM=-105; DM=-105; MA /I: B1=0; BI=-105; BD=-105; MA A B D E F G H I K L M N P Q R S T V W Y MA /M: SY='I'; M= -8,-29,-34,-26, 3,-34,-24, 34,-26, 19, 15,-24,-21,-21,-24,-19, -8, 25,-19, 3; MA /M: SY='N'; M= 0, 14, 10, 1,-22, -1, 6,-23, -4,-26,-17, 20,-14, -1, -6, 13, 2,-20,-34,-15; MA /M: SY='E'; M= -4, 4, 7, 14,-26,-13, -7,-23, 3,-22,-16, 2, 7, 3, -3, 2, -2,-21,-30,-18; MA /M: SY='R'; M=-12, 5, 5, 7,-23,-17, 3,-24, 8,-20,-12, 7,-16, 10, 12, -2, -6,-21,-27, -9; MA /M: SY='W'; M=-16,-33,-35,-27, 13,-22,-24,-11,-18,-13,-13,-31,-27,-20,-18,-30,-21,-18, 97, 25; MA /M: SY='V'; M= 1,-29,-31,-28, -1,-30,-29, 31,-22, 13, 11,-27,-27,-26,-22,-12, -2, 41,-27, -8; MA /M: SY='L'; M= -8,-29,-31,-22, 9,-30,-21, 23,-27, 37, 20,-28,-28,-21,-20,-25, -8, 17,-20, -1; MA /M: SY='T'; M= 2, -1, -9, -9,-11,-17,-19,-10,-10,-13,-11, 1,-11, -9,-10, 23, 43, 0,-32,-12; MA /M: SY='A'; M= 45, -9,-19,-10,-20, -2,-15,-11,-10,-11,-10, -9,-11, -9,-19, 10, 1, -1,-21,-18; MA /M: SY='A'; M= 40, -9,-17, -8,-21, 5,-18,-14, -9,-13,-12, -8,-11, -9,-16, 9, -2, -5,-21,-21; MA /M: SY='H'; M=-18, 0, 0, 1,-21,-19, 89,-29, -8,-21, -1, 9,-19, 11, 0, -7,-17,-29,-30, 16; MA /M: SY='C'; M= -9,-18,-28,-29,-20,-29,-29,-29,-29,-20,-19,-18,-39,-29,-29, -9, -9, -9,-49,-29; MA /I: E1=0; IE=-105; DE=-105; // score/threshold

4. Some statistics 15 most common domains for H. sapiens (Incomplete) Immunoglobulin and major histocompatibility complex domain Zinc finger, C2H2 type Eukaryotic protein kinase Rhodopsin-like GPCR superfamily Pleckstrin homology (PH) domain Zinc finger, RING type Src homology 3 (SH3) domain RNA-binding region RNP-1 (RNA recognition motif) EF-hand family Homeobox domain Krab box PDZ domain (also known as DHR or GLGF) Fibronectin type III domain EGF-like domain Cadherin domain … http://www.ebi.ac.uk/proteome/HUMAN/interpro/top15d.html

6. Database 5: protein domain/family Contains biologically significant « pattern / profiles/ HMM » formulated in such a way that, with appropriate computional tools, it can rapidly and reliably determine to which known family of proteins (if any) a new sequence belongs to Used as a tool to identify the function of uncharacterized proteins translated from genomic or cDNA sequences (« functional diagnostic ») Either manually curated (i.e. PROSITE, Pfam, etc.) or automatically generated (i.e. ProDom, DOMO)

7. Protein domain/family db Secondary databases are the fruit of analyses of the sequences found in the primary sequence db Some depend on the method used to detect if a protein belongs to a particular domain/family (patterns, profiles, HMM, PSI- BLAST)

8. Protein domain/family db PROSITEPatterns / Profiles ProDomAligned motifs (PSI-BLAST) (Pfam B) PRINTSAligned motifs PfamHMM (Hidden Markov Models) SMARTHMM TIGRfamHMM DOMOAligned motifs BLOCKSAligned motifs (PSI-BLAST) CDD(CDART)PSI-BLAST(PSSM) of Pfam and SMART InterproInterproInterproInterpro

9. Prosite  Created in 1988 (SIB)  Contains functional domains fully annotated, based on two methods: patterns and profiles  Entries are deposited in PROSITE in two distinct files:  Pattern/profiles with the list of all matches in SWISS- PROT  Documentation 19-Oct-2002: contains 1152 documentation entries that describe 1574 different patterns, rules and profiles/matrices.

10. Diagnostic performance List of matches

11. Prosite (profile): example

12. PFAM (HMMs): an entry

13. … …

14. PFAM (HMMs): query output

15. Most protein families are characterized by several conserved motifs Fingerprint: set of motif(s) (simple or composite, such as multidomains) = signature of family membership True family members exhibit all elements of the fingerprint, while subfamily members may possess only part of it

16. ProDom consists of an automated compilation of homologous domain alignment. Jan. 2002: 390 ProDom families were generated automatically using PSI-BLAST. built from non fragmentary sequences from SWISS-PROT 39 + TREMBL - Sept, 2001

17. ProDom: query output example Your query

18. Protein domain/family: Composite databases Example: InterPro Single set of documents linked to the various methods; Will be used to improve the functional annotation of SWISS-PROT (classification of unknown protein…) The release (sept 2002) contains 5875 entries, representing 1272 domains, 4491 families, 97 repeats and 15 post- translational modification sites.

19. InterPro: www.ebi.ac.uk/interpro