The SBASE protein domain library, release 6.0: a collection of annoted protein sequence segments

 1999 Ox o d Uni e si y P ess 257–259 Nucleic Acids Resea ch, 1999, Vol. 27, No. 1 The SBASE p o ein domain lib a y, elease 6.0: a collec ion o anno a ed p o ein sequence segmen s János Mu ai1, K is ian Vlaho icek1, End e Ba a2, Csaba Szepes á i3, C is ina Aca inei1 and Sándo Pongo 1,2,* 1In e na ional Cen e o Gene ic Enginee ing and Bio echnology, A ea Science Pa k, 34012 T ies e, I aly, 2ABC Ins i u e o Biochemis y and P o ein Resea ch, 2100 Gödöllö, Hunga y and 3Resea ch G oup on A i icial In elligence, Józse A ila Uni e sis y, 6700 Szeged, Hunga y Recei ed Oc obe 2, 1998; Accep ed Oc obe 7, 1998 ABSTRACT The six h elease o he SBASE p o ein domain lib a y sequences con ains 130 703 anno a ed and c oss e e - enced en ies co esponding o s uc u al, unc ional, ligand-binding and opogenic segmen s o p o eins. The en ies we e g ouped based on s anda d names (2312 g oups) and u he classi ied on he basis o he BLAST simila i y (2463 clus e s). Au oma ed sea ch- ing wi h BLAST and a new sequence-plo ep esen a- ion o local domain simila i ies a e a ailable a he WWW-se e h p://www.icgeb. ies e.i /sbase . A mi o si e is a h p://sbase.abc.hu/sbase . The da abase is eely a ailable by anonymous ‘ p’ ile ans e om p.icgeb. ies e.i INTRODUCTION De ec ion o domains in newly de e mined sequences is usually based on pa e n collec ions ha con ain consensus ep esen a ion domain ypes deduced om mul iple alignmen s. Consensus desc ip ions come in di e en a ie ies such as egula exp ess- ions, sequence p o iles, hidden Ma ko models, e c. De elop- men o such a consesnsus desc ip ion equi es expe ise and ca e ul judgemen hence pa e n collec ions can ha dly keep pace wi h he low o new genome da a. Ano he p oblem is he ine i able s a is ical bias o he consensus. Namely, a ypical domains o which he e a e oo ew known examples, may no i well wi h a consensus pa e n de eloped wi h a nume ous da ase o simila domains. Finally, he e a e domain ypes o which i is no easy o de elop consensus ep esen a ions because o weak simila i y. SBASE is a collec ion o p o ein domain sequences designed o acili a e de ec ion domain homologies wi hou he abo e p oblems (1,2). He e he me hod o domain ecogni ion is da abase sea ch a he han pa e n sea ch, so a ypical and ypical domains a e equally well ecognized. The unde lying da abase, SBASE is p ep ocessed by BLAST simila i y sea ch (3) and he simila i y g oups ( ha can be bes pic u ed as densely connec ed g aphs) o m he basis o domain ecogni ion. Table 1. Inc ease o da a in SBASE 6.0 The cu en elease 6.0 o SBASE con ains o e 100 000 anno a ed p o ein sequence segmen s consis en ly named by s uc u e, unc ion, biased composi ion, binding-speci ici y and/ o simila i y o o he p o eins. The main de elopmen s wi h espec o he p e ious elease can be summa ized as ollows. (i) Release 6.0 con ains 130 703 sequence en ies, 63% mo e han elease 5.0 (Table 1). (ii) All eco ds a e now p o ided wi h s anda d names and an e o was made o use domain names also used by o he squence da abases and pa e n collec ions like P osi e (4) and PFAM (5). (iii) The en ies we e g ouped based on s anda d names (2312 g oups) and hose wi h a leas h ee en ies (1039 g oups) we e u he classi ied on he basis o he BLAST simila i y. A o al o 2463 clus e s wi h a leas h ee membe s a e deposi ed in o a sepa a e da abase, SBASE-CLUSTERS, which is now a ailable h ough anonymous p as well as h ough links on he WWW-se e (a desc ip ion o he clus e ing p ocedu e is gi en a he web-si e). Wi hin each s anda d name g oup he clus e s a e numbe ed, in such a way ha clus e s wi h mo e in e -membe simila i y ha e la ge numbe s. (i ) A new g aphic ou pu acili y is added o he se e whe eby local domain simila i y can be plo ed along he sequence. DESCRIPTION OF THE DATA De ini ion o p o ein domains Domains included in SBASE a e p o ein sequence segmen s wi h known s uc u e and/o unc ion. The main en y classes a e summa ized in Table 2. The bounda ies o he domains a e ei he *To whom co espondence should be add essed a : ICGEB, A ea Science Pa k, 34012 T ies e, I aly. Tel: +39 040 375 7300; Fax: +39 040 226 555; Email: [email p o ec ed] by gues on Oc obe 8, 2015h p://na .ox o djou nals.o g/Downloaded om Nucleic Acids Resea ch, 1999, Vol. 27, No. 1 258 Table 2. Examples o domains in SBASE 6.0 Table 3. C oss- e e ences o o he da abases in SBASE as p e iously de ined in he o iginal publica ions o de e mined by homology o domains wi h known bounda ies. In his elease, he bounda ies used by PFAM (5) we e adop ed o a numbe o domain ypes. Sou ce and o igin o da a SBASE da a o igina e om h ee main sou ces: (i) om he SWISS-PROT p o ein sequence da abank (6); (ii) om he P o ein Sequence Da abase o he PIR In e na ional P o ein sequence da abase (PIR) (7); and (iii) om he li e a u e. F om a o al o 130 703 eco ds in SBASE 6.0, 96 305 (73%), 27 089 (21%) and 6656 (5%) a e o euka yo ic, p oka yo ic and i al o igin, espec i ely. Domain sizes a y in leng h be ween 5 and 1000 amino acids. Redundancy o sequences in SBASE 6.0 is kep a a minimal le el. In some cases, he domain de ini ions o e lap. C oss- e e ences SBASE 6.0 has c oss- e e ences o se e al p o ein and nucleic acid da abanks, as well as o he PROSITE (4), PRINTS (8), PRODOM (9) and BLOCKS (10) da abases (Table 3). In each eco d, he DR-lines con ain he c oss- e e ence da a. Reco d s uc u e The o ma o SBASE 6.0 (Fig. 1) ollows ha o he EMBL and SWISS-PROT da abases and can be di ec ly o ma ed unde he GCG package The ield ypes used a e lis ed in Table 4. The Figu e 1. A sample en y om he SBASE 6.0 p o ein domain lib a y. An annexin epea domain. The unde lined i ems a e linked in he SBASE Wo ld Wide Web se e so ha he co esponding eco ds can be iewed on he sc een by ‘clicking’ on hem. Table 4. Types o commen lines in SBASE 6.0 eco ds clus e s o which a sequence belongs a e de e mined by (i) he s anda d name and (ii) he (op ional) subclass numbe included in he CL ield, e.g. ANNEXINS/8 ( he CE ield o p e ious eleases is now abandoned). DISTRIBUTION AND ACCESS Dis ibu ion SBASE 6.0 (23 Oc obe , 1998) is dis ibu ed by anonymous ‘ p’ ile ans e om p.icgeb. ies e.i . The comple e da abase (including he eco ds and lis o clus e s), is 75 Mb, i s comp essed o m is 8.3 Mb. Access by WWW: eco d e ie al and BLAST sea ch SBASE 6.0 and SBASE-CLUSTERS can be sea ched a he WWW-se e h p://base.icgeb. ies e.i /sbase and a he mi o si e h p://sbase.abc.hu/sbase . Reco d e ie al is wi h he SRS sys em. A p esen , c oss- e e ences o SBASE-CLUSTERS, EMBL, MEDLINE, MIM, PRINTS, PRODOM, PROSITE and SWISS-PROT can be di ec ly accessed h ough he WWW- se e . P edic ion o domain homologies ia BLAST sea ching is possible ei he by (i) unning a sea ch agains SBASE, o (ii) unning a sea ch agains SWISS-PROT and ep ocessing he sea ch ou pu (11,12). In he ou pu o he la e , local domain simila i ies a e also g aphically ep esen ed as a sequence-plo (Fig. 2). by gues on Oc obe 8, 2015h p://na .ox o djou nals.o g/Downloaded om 259 Nucleic Acids Resea ch, 1994, Vol. 22, No. 1 Nucleic Acids Resea ch, 1999, Vol. 27, No. 1 259 Figu e 2. (A) G aphic ou pu o he domain simila i y se e (www. icgeb. ies e.i /sbase ) in esponse o he que y sequence C1S_HUMAN om SWISS-PROT. The known domain s uc u e o his que y is CUB-EGF-CUB- SUSHI-SUSHI-SPR (whe e S = signal, P = p opep ide, SPR = se ine p o ease). The oupu shows he plo o he BLAST simila i ies along wi h he SBASE s anda d names. A ows ha e been added o help iden i ica ion in black and whi e (o iginal is in colo ). (B) Ou pu o he domain homology WWW se e (www.icgeb. ies e.i /sbase ) in esponse o he annexin sequence shown in Figu e 1 (de ail). NSD: numbe o signi ican simila i ies ound in he BLAST ou pu ; GN.: numbe o he gi en domain occu ing in he da abase; Sum.Sco e: cumula i e sum o BLAST sco es belonging o a domain-name in he ou pu ; O e lap Max: maximum simila i y sco e ound (11). The se e ou pu con ains alignmen s p o ided wi h anno a ions and a de ailed explana ion abou e alua ion (no shown). Ci a ion Use s o SBASE and o he WWW/Email se e s a e asked o ci e his a icle in hei publica ions. ACKNOWLEDGEMENTS SBASE was es ablished in 1990 and is main ained collabo a i e- ly by he In e na ional Cen e o Gene ic Enginee ing and Bio echnology, T ies e, I aly and he ABC Ins i u e o Biochem- is y and P o ein Resea ch, Gödöllö, Hunga y. The au ho s wish o hank he suppo o EMBne , he Eu opean Molecula Biology Ne wo k. 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