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Q99986

- VRK1_HUMAN

UniProt

Q99986 - VRK1_HUMAN

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Protein

Serine/threonine-protein kinase VRK1

Gene

VRK1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Serine/threonine kinase involved in Golgi disassembly during the cell cycle: following phosphorylation by PLK3 during mitosis, required to induce Golgi fragmentation. Acts by mediating phosphorylation of downstream target protein. Phosphorylates 'Thr-18' of p53/TP53 and may thereby prevent the interaction between p53/TP53 and MDM2. Phosphorylates casein and histone H3. Phosphorylates BANF1: disrupts its ability to bind DNA, reduces its binding to LEM domain-containing proteins and causes its relocalization from the nucleus to the cytoplasm. Phosphorylates ATF2 which activates its transcriptional activity.6 Publications

Catalytic activityi

ATP + a protein = ADP + a phosphoprotein.1 Publication

Enzyme regulationi

Active in presence of Mn2+, Mg2+ and Zn2+, but is not functional with Ca2+ or Cu2+. Has a higher affinity for Mn2+ than for Mg2+. RAN inhibits its autophosphorylation and its ability to phosphorylate histone H3.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei71 – 711ATPPROSITE-ProRule annotation
Active sitei177 – 1771Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi43 – 519ATPPROSITE-ProRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. histone kinase activity (H3-S10 specific) Source: UniProt
  3. histone kinase activity (H3-T3 specific) Source: UniProt
  4. nucleosomal histone binding Source: UniProt
  5. protein kinase activity Source: UniProt
  6. protein serine/threonine kinase activity Source: UniProtKB

GO - Biological processi

  1. Golgi disassembly Source: UniProtKB
  2. histone H3-S10 phosphorylation Source: UniProt
  3. histone H3-T3 phosphorylation Source: UniProt
  4. mitotic cell cycle Source: Reactome
  5. mitotic nuclear division Source: UniProtKB-KW
  6. mitotic nuclear envelope disassembly Source: Reactome
  7. mitotic nuclear envelope reassembly Source: Reactome
  8. protein autophosphorylation Source: UniProtKB
  9. protein phosphorylation Source: UniProt
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Serine/threonine-protein kinase, Transferase

Keywords - Biological processi

Cell cycle, Cell division, Mitosis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiREACT_160242. Initiation of Nuclear Envelope Reformation.
REACT_160251. Clearance of Nuclear Envelope Membranes from Chromatin.
SignaLinkiQ99986.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine/threonine-protein kinase VRK1 (EC:2.7.11.1)
Alternative name(s):
Vaccinia-related kinase 1
Gene namesi
Name:VRK1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 14

Organism-specific databases

HGNCiHGNC:12718. VRK1.

Subcellular locationi

Cytoplasm. Nucleus. Cytoplasmcytoskeletonspindle By similarity
Note: Dispersed throughout the cell but not located on mitotic spindle or chromatids during mitosis.

GO - Cellular componenti

  1. cytoplasm Source: HPA
  2. cytoskeleton Source: UniProtKB-KW
  3. cytosol Source: Reactome
  4. Golgi stack Source: UniProtKB
  5. nucleolus Source: HPA
  6. nucleoplasm Source: Reactome
  7. nucleus Source: UniProt
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Nucleus

Pathology & Biotechi

Involvement in diseasei

Pontocerebellar hypoplasia 1A (PCH1A) [MIM:607596]: A disorder characterized by an abnormally small cerebellum and brainstem, central and peripheral motor dysfunction from birth, gliosis and spinal cord anterior horn cells degeneration resembling infantile spinal muscular atrophy. Additional features include muscle hypotonia, congenital contractures and respiratory insufficiency that is evident at birth.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi14 – 141S → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi102 – 1021T → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi125 – 1251S → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi150 – 1501S → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi158 – 1581S → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi179 – 1791K → A: Does not affect phosphorylation at S-342. 1 Publication
Mutagenesisi239 – 2391S → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi305 – 3051T → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi312 – 3121T → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi342 – 3421S → A: Abolishes phosphorylation by PLK3 and induction of Golgi fragmentation during mitosis. Strongly reduced autophosphorylation. 2 Publications
Mutagenesisi353 – 3531T → A: Strongly reduced autophosphorylation. 1 Publication
Mutagenesisi355 – 3551T → A: Does not abolish autophosphorylation. 1 Publication
Mutagenesisi390 – 3901T → A: Does not abolish autophosphorylation. 1 Publication

Organism-specific databases

MIMi607596. phenotype.
Orphaneti2254. Pontocerebellar hypoplasia type 1.
PharmGKBiPA37330.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 396396Serine/threonine-protein kinase VRK1PRO_0000086803Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei342 – 3421Phosphoserine; by PLK32 Publications
Modified residuei355 – 3551Phosphothreonine; by autocatalysis1 Publication

Post-translational modificationi

Autophosphorylated at various serine and threonine residues. Autophosphorylation does not impair its ability to phosphorylate p53/TP53. Phosphorylation by PLK3 leads to induction of Golgi fragmentation during mitosis.4 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ99986.
PaxDbiQ99986.
PeptideAtlasiQ99986.
PRIDEiQ99986.

PTM databases

PhosphoSiteiQ99986.

Expressioni

Tissue specificityi

Widely expressed. Highly expressed in fetal liver, testis and thymus.1 Publication

Gene expression databases

BgeeiQ99986.
CleanExiHS_VRK1.
GenevestigatoriQ99986.

Organism-specific databases

HPAiHPA000660.
HPA017929.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
ATF2P153365EBI-1769146,EBI-1170906
COILP384329EBI-1769146,EBI-945751
JUNP054124EBI-1769146,EBI-852823
PLK3Q9H4B412EBI-1769146,EBI-751877
RANP6282612EBI-1769146,EBI-286642
TP53P046379EBI-1769146,EBI-366083
TP53BP1Q128888EBI-1769146,EBI-396540

Protein-protein interaction databases

BioGridi113282. 18 interactions.
IntActiQ99986. 14 interactions.
MINTiMINT-3060185.
STRINGi9606.ENSP00000216639.

Structurei

Secondary structure

1
396
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni2 – 43
Beta strandi11 – 133
Beta strandi22 – 243
Beta strandi28 – 303
Beta strandi36 – 427
Beta strandi46 – 494
Beta strandi50 – 567
Beta strandi59 – 613
Beta strandi67 – 748
Helixi78 – 9013
Helixi93 – 10210
Beta strandi113 – 1219
Beta strandi124 – 1329
Beta strandi134 – 1374
Helixi138 – 1447
Turni145 – 1473
Helixi151 – 17020
Helixi180 – 1823
Beta strandi183 – 1886
Beta strandi193 – 1953
Helixi198 – 2003
Beta strandi202 – 2054
Helixi206 – 2083
Turni225 – 2273
Helixi230 – 2334
Helixi240 – 25617
Helixi262 – 2643
Helixi268 – 28013
Helixi282 – 2898
Beta strandi291 – 2944
Helixi297 – 30711
Beta strandi311 – 3133
Helixi317 – 33014
Beta strandi355 – 3573

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2KTYNMR-A1-360[»]
2KULNMR-A1-360[»]
2LAVNMR-A1-361[»]
2RSVNMR-A1-396[»]
3OP5X-ray2.40A/B/C/D3-364[»]
ProteinModelPortaliQ99986.
SMRiQ99986. Positions 1-396.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ99986.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini37 – 317281Protein kinasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 protein kinase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG330134.
GeneTreeiENSGT00760000119295.
HOGENOMiHOG000069991.
HOVERGENiHBG007532.
InParanoidiQ99986.
KOiK08816.
OMAiYCMVQWL.
OrthoDBiEOG7KSX83.
PhylomeDBiQ99986.
TreeFamiTF106473.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view]
PfamiPF00069. Pkinase. 1 hit.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q99986-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPRVKAAQAG RQSSAKRHLA EQFAVGEIIT DMAKKEWKVG LPIGQGGFGC
60 70 80 90 100
IYLADMNSSE SVGSDAPCVV KVEPSDNGPL FTELKFYQRA AKPEQIQKWI
110 120 130 140 150
RTRKLKYLGV PKYWGSGLHD KNGKSYRFMI MDRFGSDLQK IYEANAKRFS
160 170 180 190 200
RKTVLQLSLR ILDILEYIHE HEYVHGDIKA SNLLLNYKNP DQVYLVDYGL
210 220 230 240 250
AYRYCPEGVH KEYKEDPKRC HDGTIEFTSI DAHNGVAPSR RGDLEILGYC
260 270 280 290 300
MIQWLTGHLP WEDNLKDPKY VRDSKIRYRE NIASLMDKCF PEKNKPGEIA
310 320 330 340 350
KYMETVKLLD YTEKPLYENL RDILLQGLKA IGSKDDGKLD LSVVENGGLK
360 370 380 390
AKTITKKRKK EIEESKEPGV EDTEWSNTQT EEAIQTRSRT RKRVQK
Length:396
Mass (Da):45,476
Last modified:May 1, 1997 - v1
Checksum:i5640C624BF059949
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB000449 mRNA. Translation: BAA19108.1.
BC103761 mRNA. Translation: AAI03762.1.
BC112075 mRNA. Translation: AAI12076.1.
BC113510 mRNA. Translation: AAI13511.1.
CCDSiCCDS9947.1.
RefSeqiNP_003375.1. NM_003384.2.
UniGeneiHs.422662.

Genome annotation databases

EnsembliENST00000216639; ENSP00000216639; ENSG00000100749.
GeneIDi7443.
KEGGihsa:7443.
UCSCiuc001yft.3. human.

Polymorphism databases

DMDMi45593726.

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB000449 mRNA. Translation: BAA19108.1 .
BC103761 mRNA. Translation: AAI03762.1 .
BC112075 mRNA. Translation: AAI12076.1 .
BC113510 mRNA. Translation: AAI13511.1 .
CCDSi CCDS9947.1.
RefSeqi NP_003375.1. NM_003384.2.
UniGenei Hs.422662.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2KTY NMR - A 1-360 [» ]
2KUL NMR - A 1-360 [» ]
2LAV NMR - A 1-361 [» ]
2RSV NMR - A 1-396 [» ]
3OP5 X-ray 2.40 A/B/C/D 3-364 [» ]
ProteinModelPortali Q99986.
SMRi Q99986. Positions 1-396.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 113282. 18 interactions.
IntActi Q99986. 14 interactions.
MINTi MINT-3060185.
STRINGi 9606.ENSP00000216639.

Chemistry

BindingDBi Q99986.
ChEMBLi CHEMBL1293199.
GuidetoPHARMACOLOGYi 2275.

PTM databases

PhosphoSitei Q99986.

Polymorphism databases

DMDMi 45593726.

Proteomic databases

MaxQBi Q99986.
PaxDbi Q99986.
PeptideAtlasi Q99986.
PRIDEi Q99986.

Protocols and materials databases

DNASUi 7443.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000216639 ; ENSP00000216639 ; ENSG00000100749 .
GeneIDi 7443.
KEGGi hsa:7443.
UCSCi uc001yft.3. human.

Organism-specific databases

CTDi 7443.
GeneCardsi GC14P097263.
HGNCi HGNC:12718. VRK1.
HPAi HPA000660.
HPA017929.
MIMi 602168. gene.
607596. phenotype.
neXtProti NX_Q99986.
Orphaneti 2254. Pontocerebellar hypoplasia type 1.
PharmGKBi PA37330.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG330134.
GeneTreei ENSGT00760000119295.
HOGENOMi HOG000069991.
HOVERGENi HBG007532.
InParanoidi Q99986.
KOi K08816.
OMAi YCMVQWL.
OrthoDBi EOG7KSX83.
PhylomeDBi Q99986.
TreeFami TF106473.

Enzyme and pathway databases

Reactomei REACT_160242. Initiation of Nuclear Envelope Reformation.
REACT_160251. Clearance of Nuclear Envelope Membranes from Chromatin.
SignaLinki Q99986.

Miscellaneous databases

EvolutionaryTracei Q99986.
GeneWikii VRK1.
GenomeRNAii 7443.
NextBioi 29150.
PROi Q99986.
SOURCEi Search...

Gene expression databases

Bgeei Q99986.
CleanExi HS_VRK1.
Genevestigatori Q99986.

Family and domain databases

InterProi IPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view ]
Pfami PF00069. Pkinase. 1 hit.
[Graphical view ]
SUPFAMi SSF56112. SSF56112. 1 hit.
PROSITEi PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of two novel human putative serine/threonine kinases, VRK1 and VRK2, with structural similarity to Vaccinia virus B1R kinase."
    Nezu J., Oku A., Jones M.H., Shimane M.
    Genomics 45:327-331(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    Tissue: Fetal liver.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain and Lung.
  3. "The human vaccinia-related kinase 1 (VRK1) phosphorylates threonine-18 within the mdm-2 binding site of the p53 tumour suppressor protein."
    Lopez-Borges S., Lazo P.A.
    Oncogene 19:3656-3664(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, AUTOPHOSPHORYLATION, MUTAGENESIS OF SER-14; THR-102; SER-125; SER-150; SER-158; SER-239; THR-305; THR-312; THR-355 AND THR-390.
  4. "Kinetic properties of p53 phosphorylation by the human vaccinia-related kinase 1."
    Barcia R., Lopez-Borges S., Vega F.M., Lazo P.A.
    Arch. Biochem. Biophys. 399:1-5(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT THR-355, ENZYME REGULATION.
  5. "Characterization of three paralogous members of the Mammalian vaccinia related kinase family."
    Nichols R.J., Traktman P.
    J. Biol. Chem. 279:7934-7946(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, PHOSPHORYLATION.
  6. "Human vaccinia-related kinase 1 (VRK1) activates the ATF2 transcriptional activity by novel phosphorylation on Thr-73 and Ser-62 and cooperates with JNK."
    Sevilla A., Santos C.R., Vega F.M., Lazo P.A.
    J. Biol. Chem. 279:27458-27465(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  7. "The subcellular localization of vaccinia-related kinase-2 (VRK2) isoforms determines their different effect on p53 stability in tumour cell lines."
    Blanco S., Klimcakova L., Vega F.M., Lazo P.A.
    FEBS J. 273:2487-2504(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  8. "The vaccinia-related kinases phosphorylate the N' terminus of BAF, regulating its interaction with DNA and its retention in the nucleus."
    Nichols R.J., Wiebe M.S., Traktman P.
    Mol. Biol. Cell 17:2451-2464(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities."
    Sanz-Garcia M., Lopez-Sanchez I., Lazo P.A.
    Mol. Cell. Proteomics 7:2199-2214(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH RAN, ENZYME REGULATION.
  10. "Spinal muscular atrophy with pontocerebellar hypoplasia is caused by a mutation in the VRK1 gene."
    Renbaum P., Kellerman E., Jaron R., Geiger D., Segel R., Lee M., King M.C., Levy-Lahad E.
    Am. J. Hum. Genet. 85:281-289(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN PCH1A.
  11. "Plk3 interacts with and specifically phosphorylates VRK1 in Ser342, a downstream target in a pathway that induces Golgi fragmentation."
    Lopez-Sanchez I., Sanz-Garcia M., Lazo P.A.
    Mol. Cell. Biol. 29:1189-1201(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, PHOSPHORYLATION AT SER-342, MUTAGENESIS OF LYS-179 AND SER-342.
  12. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-342, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  13. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "Human vaccinia-related kinase 1."
    Structural genomics consortium (SGC)
    Submitted (SEP-2010) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 3-364 IN COMPLEX WITH INHIBITOR.
  15. "NMR solution structure of human vaccinia-related kinase 1 (VRK1) reveals the C-terminal tail essential for its structural stability and autocatalytic activity."
    Shin J., Chakraborty G., Bharatham N., Kang C., Tochio N., Koshiba S., Kigawa T., Kim W., Kim K.T., Yoon H.S.
    J. Biol. Chem. 286:22131-22138(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR, CATALYTIC ACTIVITY, MUTAGENESIS OF SER-342 AND THR-353, AUTOPHOSPHORYLATION.

Entry informationi

Entry nameiVRK1_HUMAN
AccessioniPrimary (citable) accession number: Q99986
Secondary accession number(s): Q3SYL2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2003
Last sequence update: May 1, 1997
Last modified: October 29, 2014
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 14
    Human chromosome 14: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Human and mouse protein kinases
    Human and mouse protein kinases: classification and index
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3