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P53632 (PAP2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Poly(A) RNA polymerase protein 2

EC=2.7.7.-
Alternative name(s):
DNA polymerase kappa
DNA polymerase sigma
Topoisomerase 1-related protein TRF4
Gene names
Name:PAP2
Synonyms:TRF4
Ordered Locus Names:YOL115W
ORF Names:O0716, HRC584
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length584 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalytic subunit of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Polyadenylates RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. TRF4 is also required for proper nuclear division in mitosis, DNA damage repair and sister chromatid cohesion. Involved in the regulation of histone mRNA levels. May mediate mitotic chromosome condensation. Ref.1 Ref.6 Ref.7 Ref.8 Ref.9 Ref.11 Ref.12 Ref.13 Ref.16 Ref.17 Ref.18 Ref.19 Ref.20 Ref.21 Ref.22 Ref.23 Ref.25

Catalytic activity

ATP + RNA(n) = diphosphate + RNA(n+1). Ref.25

Cofactor

Magnesium or manganese By similarity.

Subunit structure

Component of the TRAMP complex (also called TRF4 complex) composed of at least HUL4, MTR4, PAP2/TRF4 and either AIR1 or AIR2. Interacts with NOP53 and POL2. Interacts directly with AIR2. Ref.13 Ref.24 Ref.25

Subcellular location

Nucleus Ref.8 Ref.14.

Miscellaneous

Present with 7550 molecules/cell in log phase SD medium. Ref.15

Sequence similarities

Belongs to the DNA polymerase type-B-like family.

Contains 1 PAP-associated domain.

Caution

Was originally thought to have DNA polymerase activity.

Ontologies

Keywords
   Biological processCell cycle
Cell division
Mitosis
   Cellular componentNucleus
   LigandMagnesium
Manganese
Metal-binding
   Molecular functionNucleotidyltransferase
Transferase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological processU4 snRNA 3'-end processing

Inferred from mutant phenotype Ref.21. Source: SGD

base-excision repair

Inferred from mutant phenotype. Source: SGD

cell division

Inferred from electronic annotation. Source: UniProtKB-KW

histone mRNA catabolic process

Inferred from genetic interaction Ref.23. Source: SGD

mitosis

Inferred from electronic annotation. Source: UniProtKB-KW

nuclear polyadenylation-dependent CUT catabolic process

Inferred from mutant phenotype Ref.18. Source: SGD

nuclear polyadenylation-dependent antisense transcript catabolic process

Inferred from mutant phenotype. Source: SGD

nuclear polyadenylation-dependent mRNA catabolic process

Inferred from genetic interaction Ref.21. Source: SGD

nuclear polyadenylation-dependent rRNA catabolic process

Inferred from mutant phenotype Ref.17Ref.22. Source: SGD

nuclear polyadenylation-dependent snRNA catabolic process

Inferred from mutant phenotype Ref.17Ref.22. Source: SGD

nuclear polyadenylation-dependent snoRNA catabolic process

Inferred from mutant phenotype Ref.17. Source: SGD

nuclear polyadenylation-dependent tRNA catabolic process

Inferred from direct assay Ref.20Ref.17. Source: SGD

polyadenylation-dependent snoRNA 3'-end processing

Inferred from genetic interaction Ref.21. Source: SGD

snoRNA polyadenylation

Inferred from genetic interaction. Source: SGD

   Cellular componentTRAMP complex

Inferred from direct assay Ref.20Ref.17Ref.18. Source: SGD

nucleolus

Inferred from direct assay. Source: SGD

   Molecular function5'-deoxyribose-5-phosphate lyase activity

Inferred from direct assay. Source: SGD

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

polynucleotide adenylyltransferase activity

Inferred from direct assay Ref.25. Source: UniProtKB

protein binding

Inferred from physical interaction Ref.25. Source: UniProtKB

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 584584Poly(A) RNA polymerase protein 2
PRO_0000120314

Regions

Domain371 – 43161PAP-associated

Sites

Metal binding2361Magnesium or manganese; catalytic By similarity
Metal binding2381Magnesium or manganese; catalytic By similarity

Experimental info

Mutagenesis131 – 1333EDE → AAA in TRF4-131; slow growth.
Mutagenesis140 – 1423ERE → AAA in TRF4-140; slow growth.
Mutagenesis182 – 1854EIKD → AIAA in TRF4-182; lethal.
Mutagenesis1941R → A in TRF4-194; lethal; when associated with A-195; A-196 and A-198.
Mutagenesis195 – 1984EEIE → AIAA in TRF4-194; lethal.
Mutagenesis217 – 2193DAD → AAA in TRF4-217; slow growth.
Mutagenesis224 – 2252GS → AA in TRF4-224; lethal.
Mutagenesis236 – 2383DID → AIA in TRF4-236; lethal. Ref.9 Ref.22
Mutagenesis275 – 2773KAR → AAA in TRF4-275; temperature sensitive.
Mutagenesis2821K → A in TRF4-282; lethal; when associated with A-285.
Mutagenesis2851E → A in TRF4-282; lethal; when associated with A-282.
Mutagenesis309 – 3102RE → AA in TRF4-309; lethal.
Mutagenesis332 – 3332RR → AA in TRF4-332; temperature sensitive.
Mutagenesis3781E → A in TRF4-378; lethal; when associated with A-381.
Mutagenesis3811E → A in TRF4-378; lethal; when associated with A-378.
Mutagenesis4251D → A in TRF4-425; lethal; when associated with A-428 and A-429.
Mutagenesis428 – 4292DE → AA in TRF4-425; lethal; when associated with A-425.
Mutagenesis444 – 4452KK → AA in TRF4-444; lethal.
Mutagenesis467 – 4693KDR → AAA in TRF4-467; temperature sensitive.
Mutagenesis486 – 4872RD → AA in TRF4-486; lethal.
Mutagenesis490 – 4923DER → AAA in TRF4-486; lethal.
Mutagenesis5021E → A in TRF4-502; lethal; when associated with A-504.
Mutagenesis5041E → A in TRF4-502; lethal; when associated with A-502.
Mutagenesis508 – 5103KKR → AAA in TRF4-508; lethal.
Mutagenesis559 – 5602KR → AA in TRF4-559; slow growth.
Mutagenesis5601R → A in TRF4-559; slow growth; when associated with A-559.
Mutagenesis572 – 5743EDD → AAA in TRF4-572; slow growth. Ref.12

Secondary structure

............................................... 584
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P53632 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 8A58B29E4BFDC022

FASTA58466,031
        10         20         30         40         50         60 
MGAKSVTASS SKKIKNRHNG KVKKSKKIKK VRKPQKSISL NDENEVEILP SRNEQETNKL 

        70         80         90        100        110        120 
PKDHVTADGI LVLEHKSDDD EGFDVYDGHF DNPTDIPSTT EESKTPSLAV HGDEKDLANN 

       130        140        150        160        170        180 
DDFISLSASS EDEQAEQEEE REKQELEIKK EKQKEILNTD YPWILNHDHS KQKEISDWLT 

       190        200        210        220        230        240 
FEIKDFVAYI SPSREEIEIR NQTISTIREA VKQLWPDADL HVFGSYSTDL YLPGSDIDCV 

       250        260        270        280        290        300 
VTSELGGKES RNNLYSLASH LKKKNLATEV EVVAKARVPI IKFVEPHSGI HIDVSFERTN 

       310        320        330        340        350        360 
GIEAAKLIRE WLDDTPGLRE LVLIVKQFLH ARRLNNVHTG GLGGFSIICL VFSFLHMHPR 

       370        380        390        400        410        420 
IITNEIDPKD NLGVLLIEFF ELYGKNFGYD DVALGSSDGY PVYFPKSTWS AIQPIKNPFS 

       430        440        450        460        470        480 
LAIQDPGDES NNISRGSFNI RDIKKAFAGA FDLLTNRCFE LHSATFKDRL GKSILGNVIK 

       490        500        510        520        530        540 
YRGKARDFKD ERGLVLNKAI IENENYHKKR SRIIHDEDFA EDTVTSTATA TTTDDDYEIT 

       550        560        570        580 
NPPAKKAKIE EKPESEPAKR NSGETYITVS SEDDDEDGYN PYTL 

« Hide

References

« Hide 'large scale' references
[1]"Isolation of mutants of Saccharomyces cerevisiae requiring DNA topoisomerase I."
Sadoff B.U., Heath-Pagliuso S., Castano I.B., Zhu Y., Kieff F.S., Christman M.F.
Genetics 141:465-479(1995) [PubMed: 8647385] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]"Sequence analysis of a 44 kb DNA fragment of yeast chromosome XV including the Ty1-H3 retrotransposon, the suf1(+) frameshift suppressor gene for tRNA-Gly, the yeast transfer RNA-Thr-1a and a delta element."
Vandenbol M., Durand P., Portetelle D., Hilger F.
Yeast 11:1069-1075(1995) [PubMed: 7502582] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. expand/collapse author list , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
Nature 387:98-102(1997) [PubMed: 9169874] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[6]"Mitotic chromosome condensation in the rDNA requires TRF4 and DNA topoisomerase I in Saccharomyces cerevisiae."
Castano I.B., Brzoska P.M., Sadoff B.U., Chen H., Christman M.F.
Genes Dev. 10:2564-2576(1996) [PubMed: 8895658] [Abstract]
Cited for: FUNCTION.
[7]"A novel family of TRF (DNA topoisomerase I-related function) genes required for proper nuclear segregation."
Castano I.B., Heath-Pagliuso S., Sadoff B.U., Fitzhugh D.J., Christman M.F.
Nucleic Acids Res. 24:2404-2410(1996) [PubMed: 8710513] [Abstract]
Cited for: FUNCTION.
[8]"The topoisomerase-related function gene TRF4 affects cellular sensitivity to the antitumor agent camptothecin."
Walowsky C., Fitzhugh D.J., Castano I.B., Ju J.Y., Levin N.A., Christman M.F.
J. Biol. Chem. 274:7302-7308(1999) [PubMed: 10066793] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[9]"Pol kappa: a DNA polymerase required for sister chromatid cohesion."
Wang Z., Castano I.B., De Las Penas A., Adams C., Christman M.F.
Science 289:774-779(2000) [PubMed: 10926539] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF 236-ASP--ASP-238.
[10]"Eukaryotic DNA polymerases: proposal for a revised nomenclature."
Burgers P.M.J., Koonin E.V., Bruford E., Blanco L., Burtis K.C., Christman M.F., Copeland W.C., Friedberg E.C., Hanaoka F., Hinkle D.C., Lawrence C.W., Nakanishi M., Ohmori H., Prakash L., Prakash S., Reynaud C.-A., Sugino A., Todo T. expand/collapse author list , Wang Z., Weill J.-C., Woodgate R.
J. Biol. Chem. 276:43487-43490(2001) [PubMed: 11579108] [Abstract]
Cited for: NOMENCLATURE.
[11]"Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA."
Saitoh S., Chabes A., McDonald W.H., Thelander L., Yates J.R. III, Russell P.
Cell 109:563-573(2002) [PubMed: 12062100] [Abstract]
Cited for: FUNCTION.
[12]"Structure/function analysis of the Saccharomyces cerevisiae Trf4/Pol sigma DNA polymerase."
Wang Z., Castano I.B., Adams C., Vu C., Fitzhugh D.J., Christman M.F.
Genetics 160:381-391(2002) [PubMed: 11861546] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF 131-GLU--GLU-133; 140-GLU--GLU-142; 182-GLU--ASP-185; 194-ARG--GLU-198; 217-ASP--ASP-219; 224-GLU-SER-225; 236-ASP--ASP-238; 275-LYS--ARG-277; 282-LYS--GLU-285; 309-ARG-GLU-310; 332-ARG-ARG-333; 378-GLU--GLU-381; 425-ASP--GLU-429; 444-LYS-LYS-445; 467-LYS--ARG-469; 486-ARG--ASP-490; 491-GLU-ARG-492; 502-GLU--GLU-504; 508-LYS--ARG-510; 559-LYS-ARG-560 AND 572-GLU--ASP-574.
[13]"Saccharomyces cerevisiae DNA polymerase epsilon and polymerase sigma interact physically and functionally, suggesting a role for polymerase epsilon in sister chromatid cohesion."
Edwards S., Li C.M., Levy D.L., Brown J., Snow P.M., Campbell J.L.
Mol. Cell. Biol. 23:2733-2748(2003) [PubMed: 12665575] [Abstract]
Cited for: FUNCTION, INTERACTION WITH POL2.
[14]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed: 14562095] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[15]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed: 14562106] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[16]"Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae."
Kadaba S., Krueger A., Trice T., Krecic A.M., Hinnebusch A.G., Anderson J.T.
Genes Dev. 18:1227-1240(2004) [PubMed: 15145828] [Abstract]
Cited for: FUNCTION.
[17]"RNA degradation by the exosome is promoted by a nuclear polyadenylation complex."
LaCava J., Houseley J., Saveanu C., Petfalski E., Thompson E., Jacquier A., Tollervey D.
Cell 121:713-724(2005) [PubMed: 15935758] [Abstract]
Cited for: IDENTIFICATION IN TRAMP COMPLEX, FUNCTION OF THE TRAMP COMPLEX.
[18]"Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase."
Wyers F., Rougemaille M., Badis G., Rousselle J.-C., Dufour M.-E., Boulay J., Regnault B., Devaux F., Namane A., Seraphin B., Libri D., Jacquier A.
Cell 121:725-737(2005) [PubMed: 15935759] [Abstract]
Cited for: IDENTIFICATION IN THE TRF4 COMPLEX, MASS SPECTROMETRY, FUNCTION OF THE TRF4 COMPLEX.
[19]"Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNA polymerase activity but no DNA polymerase activity."
Haracska L., Johnson R.E., Prakash L., Prakash S.
Mol. Cell. Biol. 25:10183-10189(2005) [PubMed: 16260630] [Abstract]
Cited for: FUNCTION.
[20]"A new yeast poly(A) polymerase complex involved in RNA quality control."
Vanacova S., Wolf J., Martin G., Blank D., Dettwiler S., Friedlein A., Langen H., Keith G., Keller W.
PLoS Biol. 3:986-997(2005) [PubMed: 15828860] [Abstract]
Cited for: IDENTIFICATION IN THE TRF4 COMPLEX, MASS SPECTROMETRY, FUNCTION OF THE TRF4 COMPLEX.
[21]"Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome."
Egecioglu D.E., Henras A.K., Chanfreau G.F.
RNA 12:26-32(2006) [PubMed: 16373491] [Abstract]
Cited for: FUNCTION.
[22]"Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA."
Kadaba S., Wang X., Anderson J.T.
RNA 12:508-521(2006) [PubMed: 16431988] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF 236-ASP--ASP-238.
[23]"Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels in Saccharomyces cerevisiae."
Reis C.C., Campbell J.L.
Genetics 175:993-1010(2007) [PubMed: 17179095] [Abstract]
Cited for: FUNCTION.
[24]"Nop53p interacts with 5.8S rRNA co-transcriptionally, and regulates processing of pre-rRNA by the exosome."
Granato D.C., Machado-Santelli G.M., Oliveira C.C.
FEBS J. 275:4164-4178(2008) [PubMed: 18631361] [Abstract]
Cited for: INTERACTION WITH NOP53.
[25]"Structure and function of the polymerase core of TRAMP, a RNA surveillance complex."
Hamill S., Wolin S.L., Reinisch K.M.
Proc. Natl. Acad. Sci. U.S.A. 107:15045-15050(2010) [PubMed: 20696927] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 161-481 IN COMPLEX WITH AIR2, FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH AIR2.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U31355 Genomic DNA. Translation: AAC49091.1.
Z48149 Genomic DNA. Translation: CAA88145.1.
Z74857 Genomic DNA. Translation: CAA99134.1.
AY723865 Genomic DNA. Translation: AAU09782.1.
BK006948 Genomic DNA. Translation: DAA10668.1.
PIRS51882.
RefSeqNP_014526.1. NM_001183369.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3NYBX-ray2.70A161-481[»]
ProteinModelPortalP53632.
SMRP53632. Positions 161-481.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-4214N.
IntActP53632. 17 interactions.
MINTMINT-500696.
STRINGP53632.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOL115W; YOL115W; YOL115W.
GeneID854034.
KEGGsce:YOL115W.
NMPDRfig|4932.3.peg.5612.

Organism-specific databases

CYGDYOL115w.
SGDS000005475. PAP2.

Phylogenomic databases

eggNOGfuNOG05608.
GeneTreeEFGT00050000004816.
HOGENOMHBG395964.
OMALHVFGSY.
OrthoDBEOG43BQXK.

Gene expression databases

ArrayExpressP53632.
GenevestigatorP53632.
GermOnlineYOL115W. Saccharomyces cerevisiae.

Family and domain databases

InterProIPR002934. Nucleotidyltransferase.
IPR002058. PAP_assoc.
[Graphical view]
KOK03514.
PfamPF01909. NTP_transf_2. 1 hit.
PF03828. PAP_assoc. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio975589.

Entry information

Entry namePAP2_YEAST
AccessionPrimary (citable) accession number: P53632
Secondary accession number(s): D6W1V2
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: December 14, 2011
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families